To do this you need raycaster.
On threejs.hofk.de I have examples for beginners, partly German, partly English.
Look for raycaster - drag and drop
Note! The coordinates are stored in the local storage of the browser.
More complicated examples
Recaster MultiMaterial
modify Geo
A problem with multi material was solved by @Mugen87: [SOLVED] Raycaster - MultiMaterial
Have fun doing it. 