Hi Gunter, sorry currently there isn't any way to do it as a batch type operation, n-sided only works right now on one patch area at a time.

How many polygons do you have to do?

One thing that may speed up selection a bit is to do the extrusion as a solid, then delete the top face. Now you can use the "Select naked edges" script to select all the target edges with one keypress instead of directly selecting them. That should speed up the worst part of it. You can set up the select naked edges script on a shortcut key as described here:
http://moi3d.com/forum/index.php?webtag=MOI&msg=6051.2

- Michael