Theoretically? Sure. Practically? No.
The primary problem is not lack of knowledge about how to manipulate individual atoms, though this is very tricky and it might not currently possible to manipulate the right kind of atoms in the right kind of way for this sort of task. The central problem is one of scale. For an item like a Milky Way bar, you are talking about billions and billions of atoms. Your problem wouldn't be that the candy bar was melty, it would be that you would die thousands of years before there was enough of it put together to take a bite.
Also, the techniques for atom manipulation work reasonably well for placing atoms on some sort of substrate like printing circuits on silicone chips. When you start talking about things like assembling complex sugars atom by atom, the situation gets significantly more difficult.