You guys are right, I'm not saying you have to get rid of the substrate, or go bare bottom, but treatment is easy with bare bottom and hard with substrate. It depends on the degree of the outbreak as well. I hardly had an inch of substrate visible with the amount of hardscape and plants so I would've had to do some serious work to vacuum everywhere. A relatively bare tank may be fine with a good vacuum.
Like I said, a relapse can take a long time so it's nice to be sure. You don't want a relapse to find out you've sold or moved some fish in the mean time.
I don't know how one would do a decent vacuum unless you are sparsely planted.