As far as I know, it is not possible to remove these folders and sub-folders from KA Lite. The new software that Learning Equality is promoting allows for curation of content through their online Kolibri Studio. I learned about this recently and was able to select the Khan Academy content I wanted without all the extra stuff that comes with KA Lite to produce a cleaner interface for the user/learner to see. I’m sure this is what you are looking for. KA Lite is a one-package-serves-all way of providing off-line access to Khan Academy. Kolibri is a way to provide similar access, but with greater flexibility and control over how it is presented and managed. Maybe consider looking at Kolibri.