What we do: 
First we check the flue to see if it is dirty. If it is dirty it must be cleaned both for safe use and in order to be able to inspect the flue properly. 

If the chimney needs to be cleaned we'll seal off the front off the fireplace, etc. if necessary. Cleaning may be done from the top or bottom, depending on the type of system you have. We use large industrial vacuums specifically designed for chimney cleaning to ensure there is no mess. Once cleaning has been completed, we'll do the structural inspection.

If the chimney does not need to be cleaned we'll just do the structural inspection. This inspection basically covers the chimney/fireplace from top to bottom, inside and out to make sure that the entire system is in good shape and appears safe to use. 

Inspection only
Written structural inspection - referred to as a "20 point safety inspection."

Certification(in addition to the regular cleaning charge)
Written inspection certifying that at that time the wood burning system appears correctly installed and safe for it's intended use. Usually only requested by a Homeowner's Insurance company in connection with a stove installation, etc. Sometimes requested as part of a real estate transaction.