Well... there are 2 answers here.
If your user is a "simple" user, then the answer is removing the permission to these objects.
BUT
If you have put some "*PUBLIC" permission to these folders/appg/... then the only way to do it, if you don't want to remove the *PUBLIC permission, is to give the permission to the user and ensure that no check box are clicked (eg: for folder, just unclick the box "access") and by doing that, you give no access to the object.
Now if the user has some "admin" rights, then you cannot remove the permission to these objects, since he automatically has these permissions.
And in that case, the only way to do it, it to give the permission to the user, and ensure that no check box are clicked (eg: for folder, just unclick the box "access") and by doing that, you give no access to the object. Of course you can do that also for the "simple" user!