Join Date: Jul 2008
Location: right here right now
Things to check are brakes (rotors, pads, fluid, reservoir), steering head bearings for play, wheel bearings, front tire and wheel, suspension (primarily the front). Does it only happen when using the front brakes? What if you slow down using only the rear brake? If you try this make sure you have plenty of room. The rear brake is very weak in comparison to the front but can cause the rear wheel to lock up and cause the bike to skid. You could lose control.
Try giving more information. Does it happen when slowing from any speed? Is what you're feeling really a vibration or more of a pulsing feeling? Do the handlebars try to move from side to side?
You said you're new to riding? You should have the bike checked by a competent mechanic because anything abnormal when braking can be dangerous or become dangerous if ignored. Search this site and other motorcycling sites on the web for symptoms similar to yours for help in diagnosing and correcting the problem.
I hope this helps at least as much as Jpowell490 did.