Depending on the complexity of the object you want to put holes in, boolean can really be messy. However, if it's just putting holes in a simple rectangular cube, I'd use boolean.
Here's how:
1) Divide the polygons on each side of Operand A, the object you want holes in, so that each (in this case) cylinder will cut through a polygon and not all three cutting into one polygon.
screenshot
In my scene, I selected the top and bottom edges on both side and used CONNECT to divide the polygon. Next I used Inset.
2) Create the cylinders and COPY and INSTANCE the number of cylidners you want. In my scene I set the height segment to 1 and SIDES to 20. Then, select all the cylinders and convert them to Editable Polygon. Select one of them and ATTACH the others. Now you have one object instead of three; this will create a cleaner cut in the cube.
3) Finally, select the cube and choose Boolean. Select the cylinders for your Operand B. and It should come out like
this.
-----------
Another method of making holes is TESSELATING a polygon, COLLAPSING it, select the center vertex, CHAMFER it. Select the center polygon on both side and BRIDGE.
Here are some screenshots:
one
two
three
four
(ignore the three cubes below the main object
)
---
-kevin