I have done pretty much what you are asking about in my IKEA kitchen. As others have noted, you can't have a a counter-top micro in a cubby that tightly because of venting reasons. Our micro has about 2" on either side and on top for venting. This is probably less than the manufacturer recommends but it has been years and no problems.
Here is how it is (please note all measurements are approximate.)... We installed a 24" depth, 30" wide pantry cabinet. We fitted this with a bank of drawers 52" high. Above this we left an open space about 17" high with no drawers, and a plug in the rear. This is where the micro goes. Finally above that we have 24" cabinet doors in front of the top of the cabinet, outfitted inside with vertical dividers for baking pans and trays.
The vertical rows of holes on the inside of the cabinet bothered me so I cut a piece of poster board to cover the entire side wall of the open cubby and taped it in place until we could find some flat board trim pieces to use permanently. It worked so well we never bothered with the permanent fix. It has been over 10 years and no one knows. Fortunately my cabs are white so it was easy to match the inside.
This had worked out very well for us...
Nicole
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Foursquare with porch. nice color balance with lots of white. Nice woodwork on gable and porch.
Q