In port reshaping, you are changing the engine design in a fundamental way by changing the size and shape of the intake and exhaust ports - and hence the flow rate and timing of the engine. This changes the way the engine performs drasticly. If done well, this can get you up to and over 12BHP out of a 50cc engine.
This is a no-man's land of cracked rings, seized engines, and 'tuning' a perfectly functional engine into a boat anchor with a single stroke of the rasp.
Seriously, unless you have a bunch of spare cylinders or the know-how, you don't want to do this. This is exact science, and you can turn a brand new big bore kit into scrap metal if you don't have the right knowledge. For a more gentle engine modification, see port matching.
For more information on port reshaping, see Smitty's Cylinder Porting Guide. Also see Alexander Graham Bell's "2-Stroke performance tuning", John Robinson's "2-Stroke tuning", and "The Basic Design of Two-Stroke Engines" by Prof. Blair.
For info on port timing, see calculating port timing.