If you plan to fly to another airport in Costa Rica that is NOT an International Airport, you will need to request special permits from Civil Aviation and Customs authorities.
These permits have to be obtained once you arrive at the Airport, so you should allow enough time for processing.
You should consider that, depending on the airport, processing can take form a couple of hours up to a couple of days, so make sure that you make the corresponding arrangements depending on the processing times.

CST Flight Services (Formerly: Caribbean Sky Tours)
www.cstflightservices.com