Even with a very big decimation (0,5 %)
http://moiscript.weebly.com/uploads/3/9/3/8/3938813/rhino_scan_rem05.zip
http://moiscript.weebly.com/uploads/3/9/3/8/3938813/rhino_scan_rem5.obj

(unzip = .3dm of 44 megas for an .obj of 660 KB)

Boolean Operation takes some times! A Boolean Diff with a Simple Sphere takes 20 sec! ;)
Does it the same for you ?