Serve your time. If sentenced to prison, be a model prisoner. If you only have to do probation, be sure that you don't violate it in any way. Check in with your probation officer as required.
Live an honest life. If arrested again, for anything, the chances of you being granted a certificate of rehabilitation decrease dramatically.
Fill out the application and submit it to your county's court clerk's office. Submit any necessary paperwork (you can call ahead and ask what's required) at this time. You can also send the declaration to the prosecutor's office and ask that the district attorney accept your plea for a certificate of rehabilitation.
Find out when your court date is. You'll have to go in front of a judge to make your case. Ask if there is a fee to apply for the certificate of rehabilitation as well as any court fees.
Show up on time and dressed professionally. The judge will determine if he'll recommend that the governor grant you a pardon or not. Speak respectfully, but be firm in making your case.