Can anyone please tell me if the USB physical ports can be removed from the Raspberry Pi B+ ? I am using it in an audio app so I don't want to see them on the case.
Of course you can. Go ahead and desolder them. It should't be a problem.
Both the two double-port USB jacks and the RJ45 ethernet jack can be desoldered from the board - given careful handling and removing short circuiting solder. I mention the ethernet jack, as it is a big and ugly as the USB and might also show up on the case. If ethernet is needed and the jack needs to remain on board, however I fail to see the benefit of removing USB. I'd rather look for a case that just hides their existance.