The controller prefixes are module search paths that tells Endpoints where you have defined all your Controllers.
Endpoints will only route to Controllers defined in these prefixes. If no prefixes are defined Endpoints will check the current working directory for an importable controllers module.
Define controller prefixes is to set the environment variable ENDPOINTS_PREFIX, for example:
$ export ENDPOINTS_PREFIX=controllers
Now, when Endpoints is started it would route to any Controller class found in the controllers python module.
You can define multiple controller prefixes through the environment also:
$ export ENDPOINTS_PREFIX=foo.controllers:bar.controllers