I have a problem with the fitting of pitts style mufler in the super chipmunk cowl. I have made the appropriate openings for engine/mufler but the mufler ends are exposed well enough which I don't like. The engine is side mounted with the mufler under it.

How you guys fininsh this up...

Do you mean the exhaust tube ends? If so, cut'em off where you want them. (You'll get more residue on your plane though).
Got a pic?

No I canot cut them off as they are the ends (corners) of the main cylinder just under the engine outlet, not the exhaust pipes.

From the sounds of it you have three options. Listed from easiest to most difficult.

1. Get a dremel and grind out the cowl a little more. The muff. is under the head anyway. You really won't notice it when the plane is trolling around the sky.

2. Try a different muffler.

3. Remove the muff. and carefully grind off what you don't like-keeping very close tabs on the thickness of the area you're working on.

Sounds like a Slimline. They do have a little extra AL at the point your talking about. You can try grinding but, be careful.