Bicycle Mechanics - Stubborn Pedals

I own a Trek 4500 and am currently using a friend's old bike for parts to improve it but I am having trouble removing the pedals on both bikes.

I have taken out the bolts, but the pedals will not budge. Is there anything else I am not doing that you could suggest?

Oh and I don't know if it would make a difference but my Trek pedals are actually out of alignment so they may be damaged in some way.

If the threads are corroded or siezed, apply some penetrating agent such as light oil/solvent (WD40).
Leave the pedals for a day or 2 then remove using a long handled wrench.
The non drive side has a reverse thread so rotate clockwise to remove.

The best technique for pedal removal is to stand the bike upright and apply the brakes.
Turn the crank arm to face forward and up.
Apply the wrench to face rearwards and up.
Press down on the wrench with your foot and apply weight.

took the bolts out? are you trying to take the cranks or the pedals off?

The pedals will have flats on the inside portion of the axle. There may even be an allen head on the end you can see by looking at the back of the crankarm. Sounds like yer trying to get the cranks themselves off. After removing the bolts you'll need a crank extractor to get them off the bottom bracket spindle, which yer lbs will have if you dont. As far as pedal removal techinique I find it sufficient to hold the wrench in one hand and brace the opp. crankarm with the other. Should give you sufficient torque to ease even stubborn pedal threads. Just remember that the left pedal is LH thread or opposite from 'normal'. Have fun

Ammonia is the release agent for seized aluminum-steel joints. Boiling water will also expand the aluminum sufficiently to make removal of the steel pedal easier.