How do I add lots of holes into the surface of my model? I am 3d printing a ds9 model from thingiverse, but I would like to add all the holes for the fibre optic threads to my mesh surface. 

This Commercial kit has over 1000 holes to drill for fibre optics. I've found a company who has Drill hole plans that I can use as a texture map. I would like to shortcut the drilling hole step, and am looking for a method to create lots of holes from the texture map.

Note: I already have a method to create the shell/hollow model, as well as a method to cut the model in half.
If the drill hole plans are in vector already convert the file to .svg.

If the hole plans are not vector.
Convert the holes to vector using Inkscape, Illustrator, etc...
Once everything is traced/converted save this file as .svg.

When you have a usable .svg file.
Open Blender and choose File/Import/Paths
Choose your .svg
With the newly created path selected in blender.
Go to the curve options and raise the extrude value up.
If the alignment is good, use the boolean modifier to "cut" the holes. Example

If not already vector &amp; automated methods fail. Instead of manually tracing the holes. You may be best off duplicating a cylinder, of the correct size, &amp; placing the duplicates where need be. Using the mirror modifier if and/or where possible. Then use the boolean modifier as mentioned previously.