Just keep exercising those fingers. Whenever you've got a spare moment, pick up your guitar and do a bit of a workout with the techniques that you find most difficult - barre chords, double-stops, scales, whatever is challenging you. Even if performing one of these techniques necessitates you contorting your fretting hand into some excruciatingly uncomfortable position, do so! Practice that position until it doesn't hurt any more! :D

The key is, persist, and before you know it, your fingers will be lean, mean fretting machines.