I was thinking of a clockwork/mad engineering theme, but it could be converted into a scavenger/improvised technology theme I suppose.
And those fractal things wouldn't work. Well, they might, but the technology involved would mean that they would be facing things that render them ineffective. Obviously to function they need some sort of defensive energy field to deal with inertia(which will still ruin their day, just not fatally. They WILL need to equalise velocities in order to use NANOmanipulators of all things and actually retain any of the material) which mean that you can just turn on a bigger field to keep them at a safe distance, and crush them into a solid block while you are at it. And then there is the issue of actually touching incoming projectiles. It sounds as though tracer rounds could mission-kill them without difficulty.
As for beating flame-throwers? Nanites are extremely slow. Best mobility they are going to get is insane tech(which means the opposition gets lava armour and E.M.P. bullets) or jumping, which is nice and all but requires an inordinate amount of prep-time and from a nanite still means very little distance covered. Not to mention that disassembling something on a molecular scale is extremely energy intensive, and nanites don't have any space for energy acquisition, so a splotch on a flamethrower will still leave you with hours, if not days of flame-throwing at its friends, by which time the battle is long-over and everyone is back in decontamination...
They would, though, be a good terror weapon, what with the whole invisibility thing, and also good over large undefended areas. They would be a good choice for ecological destruction if you aren't in any hurry...