I believe it's called leeching or sick glass. They can only be removed by tumbling or a powerful acid bath, which is extremely dangerous. I can't remember what acid is used.
I dig bottles in an old dump where hot ash was also mixed in. This leaves scars or white blotches on the bottles. Some also have contents that evaporated away and left hard water residue on the glass. I soak the bottles in soapy water and use 000 steel wool to polish out andy of the set in hard water and heat stains. This is hard work and takes time so I only do it to bottles of value. As I stated in your other post let us know what bottles youve got there so we can give you an idea of thier value thus letting you know if it would be wothwile to invest your time or money on cleaning these bottles..
To clean the inside of the bottle I use 000 steel wool and a plastic coat hanger to press it against the inside of the bottle (Break the coat hanger at the corners so that you have a "stick" with a little hook shape on the end). The plastic wont hurt the glass and the 000 steel wool will not hurt the glass either. If you'd like Ill send some pics of this "device".