When you create a template that includes project content, each tool brings in its own kind of structure, depending on the type of content it manages.
Some tools, such as Documents, Tasks, and File Releases, can be thought of as folders that contain individual items, subfolders, or both.
For example, the Documents tool has a Root Folder, inside which you can create a tree of subfolders to organize your documents according to your project's needs. Every document lives inside one of these folders.
In a project that has been in use for any significant time, users have probably created some number of documents, which they have shared by adding them to a folder in the Documents tool. When you create a project template from that project, you can choose to include those documents in the project template or not.
The Reports and Wiki tools are not organized in folders. When you include the content from these tools in a template, new projects created from that template include a flat collection of all the Wiki pages or reports in the original project, with all their text and data.