It can be a lengthy game, and a little confusing, so here's a quick gameplay video of my entry, which can give an idea of what sorts of strategies can be used to keep from running out of nanomachines, or prevent building up too much heat.

In particular, those square bacterial formations? Those are perfect. If you can get your bacteria to form some, send your machines after those!

https://www.youtube.com/watch?v=oe4ZT7dg8lM

Link to entry: https://ldjam.com/events/ludum-dare/40/nano-life