Is there any way to cut out a subject from one clip completely and paste it in front of another clip? I know you can do this filming in front of a green screen but is there any way if you didnt film the subject infront of a green screen?

The simple answer is "yes". Basically, just like green screen, you create an alpha mask to isolate your subject. Creating the mask without the chroma background is not be so easy and will depend on your footage. You need some form of compositing application e.g. After Effects. I'd probably start with a garbage matte and seeing what a luma key looks like. Whatever you can do automatically, its probably going to need a heap of tedious manual tidying up.

I have after effects and i have final cut pro. which would be the better?

If you're willing to spring for AE CS5, the new Rotobrush tool is your best bet.
Adobe rotobrush video (http://tv.adobe.com/go/4921/)
I gave it a quick try last night and yes, it really does work!

Ah thankyou, thats exactly what I was looking to do