Filing of a business certificate at the local Town Clerk's office does NOT protect your name as it does a corporation filing, or a trademark registration (which is done through the State). It also does not give you permission to operate a business in the town. It only registers your mimic (some states refer to these as fictitious name documents). In order to locally operate a business in the town you must get the appropriate permits, permissions, variances, etc. that are required by the issuing departments of the town through the Licensing Agent.
A business certificate primarily allows consumers and/or creditors to identify the names of the actual owners of a business. Therefore, a city or town clerk may even accept more than one certificate with an identical business name in order to provide this public record.