I have two invisible bumps on the side of my foot and right beside it is a callus. the two bumps itch very badly.

Look closer....: It might be that you are applying a little too much vanishing cream to the area and now the bumps have become invisible. ( I couldn't resist it.) Callus formation is either from pressure, foreign body or possibly confused with a wart. Itching is usually as a result of contact with an irritant or a skin infection. Without a picture, your best bet is to start with visit to a foot specialist.