Just bolt the rod back to the pedal and pull. or feets uses a rolling jack to do it, but don't remember. Careful if you put it in to do it to make sure fluid doesn't spew.
i remove the master cylinder with rod attached and use an xacto knife with a pointed blade to cut out the rubber holding the rod in. doesn't tear up any parts, other than the rubber piece.
remove it with the rod attached, put the rod in a bench vise and use a big screwdriver to pop them apart,OR put the cylinder in the vise and put a long rod, screwdriver, etc thru the hole and give it a yank..Some lube like PB blaster will help.
If you have a floor jack with a removable saddle, stick the pushrod down through the saddle hole and put a long screwdriver through the hole, perpendicular to the jack. A couple of easy pumps on the jack handle and the pushrod will pop right out.