I want to use the 'Numbers' preset/effect to create a counter in After Effects. This is no problem.
But when I draw a mask over part of the counter it doesn't mask anything? Help
That has to do with render order. The mask is considered before the effect is applied. You need to precomp the layer, move the effect in the precomp and apply the mask on the precomp. For more infos see
What Mathias said - pre-compose or use a second layer (solid) to which you apply the mask as a track matte for your Numbers effect.