1. how do i build an atomsmasher?
Dig a room somewhere out of the way in your fortress. Build a raising drawbridge ('g' under the build menu, and to make a raising bridge select a direction) filling the room. The direction it raises doesn't matter for this. The material also doesn't matter.
Create a mechanic's workshop. Build three mechanisms. Make one mechanism in to a lever (press 'b', then 'T', then 'l'). Link that lever to the bridge with the remaining two mechanisms.
Once the bridge is built and linked to the lever block off the passage to the bridge room with a wall or locked door. You don't want anyone wandering in there by accident.
Dig a tunnel on the level above the drawbridge. Channel out one hole in the floor directly above the bridge. Designate a dump zone (press 'i', select the zone area, enable as a garbage dump) on one or more square adjacent the zone.
Pull the lever once to raise the drawbridge. Your atomsmasher is now ready for use.
2. how do i operate it?
Designate the object you want destroyed for dumping. A dwarf will grab it, take it to the garbage zone, and throw it in. It will land under the raised drawbridge. Tell a dwarf to pull the lever. The bridge will lower and destroy the dumped object. Pull the lever again to raise the bridge.
3. is it still possible to use the items after they got atomsmashed?
No. Atomsmashed objects are permanently gone. That's the whole point.