We will get commercial goods (value: approx. 2000 USD) via EMS from outside Thailand. We do have import licence/paperless, but usually the courier (like UPS) or brokers are doing the customs clearance. Is it difficult/possible to do the "customs" clearance for EMS. What exactly must be done and must presented?

Once you receive notification from the Post Office that your shipment has arrived, it is possible to notify your customs broker to contact the Post Office to handle customs clearance.

Otherwise just pay whatever duty the Thai Post asks for and then go pick up the package.