I've made a screencast showing a method which will give you the results you want, ie. cylindrical holes who's axis are perpendicular to the surface.
The basic idea is to project points to the surface, then using these points to create axis that are perpendicular to the surface.
Then make a cylinder and use the 'rectangular pattern' to make a bunch of copies (faster than using copy/paste). Use the 'Align' tool to position all the cylinders over the body.
Not shown in the screencast ( which is highly edited) I made a body that could be used to combine all cylinders together as one object to be used to Cut holes in the model in one shot.
I used a decal of an isometric grid on the model and used that for a reference to locate the holes, but you could of course use other methods to do that or a different image as a decal.
Just a note: when you are Aligning the cylinders press ok once and a while, because if you are almost done and press cancel or undo you will lose all the aligning you did and have to start from the beginning.
One last thing: do half the model, once done, split the model in half and mirror the half with the holes and join the two halves together.
Athough the screencast is incomplete, it shows the concept.