Deal with it. ;-)
Since we'll be deconstructing the original, the most logical way to accomplish this is from the top down, with a plate that travels vertically instead of a carrier that moves horizontally underneath a glass platen.
That's the easy part.
The biggest problem inherent in the process is that of generating the 'null fields' without disintegrating the mechanism at the same time. The null fields will be generated for a fraction of a second, just long enough to dissociate the components of the particular atom being deconstructed at that precise moment. Thus, the null fields will be generated as a pulse, rather than a continual stream, and could concievably be focused by something along the lines of a 'magnetic lens'.
The animation below shows the process on a helium atom:
Once we've deconstructed the atom, the protons, neutrons, and electrons need to be stored somewhere. The particle collector will be connected to a conduit, the walls of which will be electromagnetically charged to repel the subatomic particles as they travel through it. The containment area will also be charged, so that the particles will tend to stay in motion instead of gathering along the walls.
Granted, this is a very simple explanation, but it should be sufficient to give an idea of how the system operates.