Not really deformed, but sure feel that way.  This is my problem...

I am a female, only 5 ft. 0 inches tall.  I have short, fat fingers.  When I attempt a barre chord, for any part of my index finger to reach the E6 string, the part of my index finger that ends up hitting the E1 string is literally halfway down past my first and second knuckle, almost at my palm (I tried to figure out where I could post a photo to link to, but I can't).  Not only is this not working now, which I would expect since I'm a beginner, but from what I can tell and what I know about physiology and mechanics, I don't know if this will EVER work. 

Also, I have this weird short thumb on the left hand (a full inch shorter than the right thumb), and I'll never be able to mute that E6 with my thumb.

My doubt comes from the whole "muscle memory" thing.  I'm just skeptical that practicing it "wrong" will ever make it right, given my physical limitation.  You people with long, thin fingers (actually long and anything) make me green with envy.

Has anyone else out there found that they were able to overcome this type of problem?  If so, how??? Because I really want to get over this problem and play those darned barres.

I really want to help with this one so here's what I tried. I fretted all 6 with my index finger and made sure I was fretting E1 with part of my palm. Now on your hand it may not work but I could still fret an F barre for example, with my middle, ring and pinky. But it wasn't easy or comfortable but then again neither were barre chords when I was beginning.

You can open a free account at photobucket do com and then you'll be able to show a pic of your hand on the fretboard. I did notice the further up I moved on the fretboard the more difficult it became.

If you're a total beginner it may not be too late to change to playing left handed. (addressing the short thumb issue here)  I know left handers that bought right handed guitars and since they were just starting off it didn't make any difference for them. This may vary from person to person but you could try flipping your guitar to the right and try chording (barre) with your right hand. A suggestion is all as I'm no physiologist or even a 'real' guitarist..yet...however, I will be and barre was impossible at first and now it's second nature after only 3 or so years of working with barre and I find myself using barre chords more and more. The attending muscles do strengthen. Some will hopefully chime in with some ideas or exercises.

Oh and it occurs to me to ask the width in inches of your guitar neck at the nut. I know a lady that has a classical guitar with a wide neck and short fingers and this is holding her back a bit though she is progressing with some encouragement.

GuitarZen