Once Cylinder is activated legally, it's going to go through regardless of the position/lack of field presence of the attacking monster. This is why you can chain Mirror Force to your own Cylinder. Mirror Force resolves destroying all attacking monsters, then Cylinder, which had a legal target at activation, blows through and does the damage. BBTD is good, Trap Jammer, 7 tools, Solemn Judgment, and Royal Decree, These are counters that come to mind right now. Book of moon, Interdimensional, compulsory, etc. won't stop it once it's activated.
Jeff