You can hide or exclude folders in my apps by either changing where the app starts inside your account or by hiding folders individually.
To change where the app starts in your account, go to the app’s settings > General > Starting Folder. Then select the folder where you want the app to start. Then hide any subfolders you do not want.
To hide individual folders and subfolders, go into the folder you want to hide and select the … menu in the upper right. Then select hide folder.