I got underneath my truck the other day and noticed that my frame has rusted through on both sides on the bottom of the rail.
Has anyone else come up with this sort of problem. If so how would I go by fixing it. Thanks.

 

I'm not certain from your post about the rust through. Where on the frame?

Lots of people, including myself, have modified, fabricated, and reproduced frames and their components. You could cut out the rusted part and "section" in a new one, fabricated one, or used one.

Just be sure that you understand: Sectioning or modification of the frame, if not done properly, could change crumple or "crash" areas that are designed to maintain the integrity of the passenger compartment, (gads, I sound like I'm giving a disclaimer???) in the event of an accident.

 

If its true that you have a rusted through section it should be repaired....this will cause a weaken frame
Take your truck to a frame shop and have the pro's look at your frame and advise you about proper repairs