Punching holes in objects

[Limiter]

I am currently researching ways to punch holes in objects cleanly.

One of the standard ways is to use boolean. But as we know, it isn't really useful because it messes up with your mesh especially if you have to punch many holes into that object.

For example, if I am modelling ceiling lights, I might punch a bunch of cylindrical holes into the ceiling to fit the lights in. But then the ceiling will have messed up mesh from all the hole punching from boolean.

Are there other ways to punch holes that are better than boolean?

edit: I watched this but it does not serve well if I want to punch complicated shapes into objects. http://www.3dtotal.com/index_tutoria...2#.T-F_WFvUCjA