There are many fuel system cleaners out there, and a few of them are actually pretty good. One that I highly recommend is Sea Foam Motor Treatment. I use this stuff in everything - my lawn mower, my motorcycle, my car, my weed eater. Basically anything with a motor I'll dump some of this in there.
Note: Link at the bottom is affiliate
Sea Foam is formulated to not damage any of your engine's internal parts. You can use it with every fill up or just every once in a while. I try to use it about once a month, but that's probably a little overkill. Most people do a can of this stuff with every oil change, which is plenty.
If you look around the web, you can see that sea foam's products are top notch. They come highly recommended by all sorts of mechanics and gear heads. My uncle first turned me on to the stuff when I bought my 1982 Kawasaki KZ 550 LTD. I only had that bike for a couple years, but when I bought it it had a lot of trouble getting tor proper amount of fuel. The carburetors were all gummed up and their was a lot of carbon buildup. Part of getting it back on the road was using a lot of sea foam to clean out the fuel system. Bike ran well when I sold it (which I still regret).
I've included a couple videos beneath the button below that prove how good Sea Foam actually is. If you feel like your bike's been running a little rough, try running a can of this through it.
Wade Thiel is the creator of Wind Burned Eyes. He is an automotive journalist and a motorcycle enthusiast who lives in Indianapolis, IN. Check him out on Twitter or read his automotive work at Web2Carz.