An After Effects project is a single file that stores compositions and references to all the source files used by footage items in that project. Compositions are collections of layers. Many layers use footage items (such as movies or still images) as a source, though some layers—such as shape layers and text layers—contain graphics that you create within After Effects.

A project file has the filename extension .aep or .aepx. A project file with the .aep filename extension is a binary project file. A project file with the .aepx filename extension is a text-based XML project file.

The name of the current project appears at the top of the application window.

A template project file has the filename extension .aet. (See Template projects and example projects.)

XML project files

Text-based XML project files contain some project information as hexadecimal-encoded binary data, but much of the information is exposed as human-readable text in string elements. You can open an XML project file in a text editor and edit some details of the project without opening the project in After Effects. You can even write scripts that modify project information in XML project files as part of an automated workflow.

Elements of a project that you can modify in an XML project file:

• Marker attributes, including comments, chapter point parameters, and cue point parameters

• File paths of source footage items, including proxies

• Composition, footage item, layer, and folder names and comments

Some strings, such as workspace and view names, are exposed as human-readable strings, but modifications made to these strings are not respected when After Effects opens the project file.

Project links embedded in QuickTime, Video for Windows files

When you render a movie and export it to a container format, you can embed a link to the After Effects project in the container file.

To import the project, import the container file, and choose Project from the Import As menu in the Import File dialog box. If the container file contains a link to a project that has been moved, you can browse to locate the project.

Create and open projects

Only one project can be open at a time. If you create or open another project file while a project is open, After Effects prompts you to save changes in the open project, and then closes it. After you create a project, you can import footage into the project.

• To create a project, choose File > New > New Project.

• To open a project, choose File > Open Project, locate the project, and then click Open.

You can also create and open a project from the Start screen.

• To create a project, click New Project.
• To open a project, click Open Project and navigate to the location of the project.
  

Jeff Almasol provides a script on his redefinery website that creates and saves a new project for each selected composition in the current project.

Template projects and example projects

A template project is a file with the filename extension .aet. You can create templates based on your projects.

When you open a template project, After Effects creates a new, untitled project based on the template. Saving changes to this new project does not affect the template project.

Often, the creator of a template project locks layers that are to be left unmodified, and leaves layers to be modified unlocked. It is a convenient way to prevent accidental or inappropriate modifications.

For more sources of After Effects example projects and template projects, see After Effects community resources on the Adobe website.

See this video tutorial by Andrew Devis on the Creative COW website for information about where to find template projects and sample expressions included with After Effects.

Open a template project

• To open a template project, choose File > Open Project. On Windows, choose Adobe After Effects Project Template from the Files Of Type menu.

Create a template project

• To convert a project to a template project, change the filename extension from .aep to .aet.
• To save a copy of a project as a template project, choose File > Save A Copy, and then rename the copy with the filename extension .aet.

Set a template for new projects

You can create a template with your preferred project settings such as color management and folder structure, and use it as a foundation for every new project you create.

To set a template for your new After Effects projects:

1. Choose Edit > Preferences > New Project.
2. Enable the New project loads template check box.
3. Click Choose Project Template and select a template file. 

Team Projects

Team Projects is a hosted collaboration service for CC enterprise and CC teams users that enables editors to seamlessly collaborate in the editing workflow in real time. Using Team Projects, editors and motion graphics artists can work simultaneously in shared team projects within Adobe Premiere Pro, After Effects, and Adobe Prelude without any additional hardware.

The project updates are securely tracked in the cloud and the source files are saved locally or in lightweight, shared proxies. Team Projects also include deep collaboration features like version control and smart conflict resolution.

• To create a team project, choose File > New > New Team Project.
• To open a team project, choose File > Open Team Project.

For detailed information on how to use Team Projects for your collaborative workflow, see Working simultaneously in shared video projects.

Convert Team Project to an Adobe After Effects Project

You can convert your Team projects to a local Adobe After Effects Project (.aep). Select Edit > Team Projects > Convert Team Project to Project.

Save and back up projects in After Effects

• To save a project, choose File > Save.
• To save a copy of the project with a new automatically generated name, choose File > Increment And Save, or press Ctrl+Alt+Shift+S (Windows) or Command+Option+Shift+S (Mac OS).
• A copy of the current project is saved in the same folder as the original project. The name of the copy is the name of the original followed by a number. If the name of the original ends with a number, that number is increased by 1.
• To save the project with a different name or to a different location, choose File > Save As > Save As. The open project takes the new name and location; the original file remains unchanged.
• To save the project as a copy in the XML project file format, choose File > Save As > Save A Copy As XML. (See About projects.)
• To save a copy of the project with a different name or to a different location, choose File > Save As > Save A Copy. The open project retains its original name and location, and a copy is created with the new settings but is not opened.
• To save a copy of a project to be opened by the previous major version, choose File > Save As > Save A Copy As <previous major version number>. (For more information, see this blog.)

To save a copy of the project and copies of assets used in the project to a single folder on disk, use the Collect Files command. (See Collect files in one location section for details).

Flowchart panel

In the flowchart for each project or composition, individual boxes (or tiles) represent each composition, footage item, and layer. Directional arrows represent the relationships between components.

Nested compositions and other elements that make up the composition appear when you expand a composition tile.

Mid-gray lines between tiles in the flowchart indicate that the Video or Audio switch for those items is deselected in the Timeline panel. Black or light gray lines indicate that the switch is selected, depending on the Brightness setting in the Appearance preferences.

• To open the project flowchart, press Ctrl+F11 (Windows) or Command+F11 (Mac OS), or click the Project Flowchart button at the top of the vertical scroll bar on the right edge of the Project panel.
• To open a composition flowchart, select the composition and choose Composition > Composition Flowchart, or click the Composition Flowchart button at the bottom of the Composition panel.
• To activate (select) an item, click its tile in the Flowchart panel.

  When you click a composition in the flowchart, it becomes active in the Project panel and the Timeline panel. When you click a layer, it becomes active in the Timeline panel. When you click a footage item, it becomes active in the Project panel.

• To customize the appearance of the flowchart, use the Flowchart panel menu and the buttons along the bottom of the panel.

• To delete elements, select them and press Delete. If the selected element is a footage item or composition, it is deleted from the project and no longer appears in the Timeline and Project panels. If the selected element is a layer, it is deleted from the composition in which it appears.
• To access the context menu for a selected element, right-click (Windows) or Control-click (Mac OS) the icon to the left of the name in the element tile. The icons have various appearances, depending on the element type, such as layers and compositions . For example, you can use the context menu for a layer to work with masks and effects, or to change switches, apply transformations, and adjust layer image quality.

Rich Young provides additional information about the Flowchart panel and the Composition Mini-flowchart on the After Effects Portal website.