Rust
 

I am trying to clean up a frame that i have and noticed some rust inside the bottom bracket shell. Is it safe to assume that the the frame has rust thoughout the inside of the frame? If so how do i ride the frame of the rust?
Does Framesaver just protect the frame from future rust?

Nah... that's a common place to have a bit of rust since water dribbles down through the other tubes to the BB shell. If flakes of rust are falling down into the BB shell from other tubes, then ya it may be really rusted out. But if it's just a bit and it appears that it CAME FROM the BB shell, I wouldn't worry much.

Before using something to prevent future rust, you might try spraying in some "Metal Prep" from the hardware store, and letting it soak well, then drain it all out. Don't rinse it with water, but let air dry. Metal Prep is a solution of phosphoric acid (& probably other stuff), so it's best to keep it off the paint (won't harm really tough paint like Imron though). The phosphoric will eat away all the rust & leave a gray/black coating on the bare steel. Once dry, then use your Framesaver™ or linseed oil, whatever.

Works for me.

Does the Metal Prep weaken the frame? From your description it sounds kind of scary.

Shouldn't hurt anything. It just eats at the rust, but takes very little to nothing from the good steel. It's intended use is prepping bare or rusted steel for painting.