Yes, 'clean' is the right word for what you do with shoes that are dirty. It's possible, but not usual, to say 'clean up'. The object of 'clean up' is usually the stuff which needs to be removed e.g. 'I must clean up that mess in the kitchen'.
No, 'void' isn't the right verb. For a bottle of shampoo, a packet of rice, or anything else of that type, the verb you want is 'empty'. For example, if you are tidying up after breakfast, you would empty the coffee cups into the sink. For a hard drive, you could say 'empty', or more likely 'wipe' or 'clear'.
'Void' is not a common verb. It's used in the sense of 'empty' in medicine/physiology, and also in other technical and scientific fields, but not in everyday English.