As long as you don't get carried away, you can grind the corners off the fins to give the cylinder a more rounded appearance. The aluminum is easy to remove with a side grinder and a 'flapper wheel' type of abrasive. The loss of cooling ability shouldn't effect the engine unless you're riding style includes long periods of idling or slow riding under a load in high ambient temperatures.
A rule of thumb in the case of a heat exchanger, which the cooling fins are, is that you can eliminate as much as 10% of the surface area without seriously compromising its ability to transfer heat, except in extreme conditions.
Tom