Is there a specific procedure for grounding a pilot?
It depends on how/why you are grounded and who does the grounding.

The FAA can legally ground you if your license gets suspended (or in rare cases completely revoked) there are formal proceedings the FAA has in place. You can find the AC that covers it here. 

AME's can can deny you a medical certificate which can prevent you from flying. In this case you are also legally grounded as you may no longer comply with FAA regulations.

AME's may also make grounding recommendations. Say you start taking a new medication that is legal on the FAA's list. The general advisory is to "see how the medication effects you" prior to getting back to flying. Often this is subjective and there is not really any hard guidance on time limits for every medication. These groundings should be self imposed by the pilot.   

You can be practically grounded by say a flight school or insurance company. This falls more into the "not fit to fly" category. Technically you are legal to fly but other practical limitations may prevent you from flying. Lets say you show up to rent a plane and you are clearly sick. You say you "feel fine" but the flight school is under no obligation to rent to you and may chose not to if they feel you are not fit to fly. 

Every pilot is responsible for a self assessment prior to making any flight to ensure they are fit to fly. Ultimately an infraction could fall under 91.13 Careless or Reckless Operation. In this case you may or may not be legal to fly but its up to you to make that self assessment and not fly.