By default, TrashMe offers to display a list of your applications installed in the default location for Mac OS X ("Applications" folder). However, if you put applications in a different folder, you can add a personal folder in the sidebar, and then list all the applications in this folder.
Note: at first launch, the folder "Downloads" is already added to the sidebar.
Click on the "+" button, just below the sidebar
Select a folder in the dialog box
Click on "Choose"
Select the folder to remove in the sidebar
Right-click this folder and choose "Delete"
Warning: this folder will be removed from the sidebar but not deleted from your computer.