FDM, ABS Post-processing methods
Your objective is quite a challenge, considering the limitations within which you have to operate. Small diameter of an appreciable length is daunting indeed.

I would consider to use a regulated heat source such as a soldering station, one with removable tips. After electing an appropriate tip to handle the dimensions, a hole drilled into the tip to accept the pin diameter and length would be the next step.

There would be consideration needed for the plastic material pushed ahead of the soldering tip, as well as angular stability while pushing the soldering iron onto the pins.

To improve these circumstances, a sharp edge ground at the end of the soldering iron tip would give a better shearing of the excess plastic. 

The temperature control would be critical to prevent destruction of the pin within the tip and to provide optimum removal via the cutting end.

Directly related to the above, but without the heat would be the equivalent tool to be used in a rotary grinder such as a Dremel. The bore of the custom-made cutter would match the pin and the sharp cutting end could also have serrations such as those found on hole-saws. Low speeds and a steady hand are required!

If either of the above suggestions do not remove sufficient plastic roughness, one would make the pins of a larger diameter and ensure that excess is removed to specifications.

EDIT: Additional thoughts. Hobby stores and online equivalents will sell very small diameter tubing. It might be an easy matter to find 2 mm inside diameter tubing of brass or even stainless steel. A few passes on a piece of sandpaper while the tubing is chucked in an electric hand drill and you have a sharp cutting edge.