I always leave my fish in. I think you can tell when they are starting to get stressed by their colour and behaviour. I have my hand in the tank and am moving things about so often they are quite accustomed to it. I only try to catch them once in a blue moon and am rather inept at it, unsurprisingly this makes them very stressed!
I think Georges point about the substrate is crucial. In additon to the fish stress I have found that if I disturb the substrate and it is really dirty it can cause a minor algae bloom. This algae bloom can appear up to 2 weeks later. I always try to make sure my tank is in good condition before doing major rescaping, so the bloom is then nothing to worry about, just some extra food for my ottos and shrimp.
I'm rarely in a rush, so rescape in stages. Maybe disturbing a foot square at a time and ensuring a large water change after each disturbance.
As an example, my last rescape was done over 4 separate days in my 160l 3footer. I replanted every single plant, repositioned all the hardscape, removed a third or so of the substrate, and repositoned the rest. I left about a third of the tank untouched each session, so the fish and shrimp could hide in this section while I was working elsewhere. Some of the time they did and some of the time they just got in my way rooting around the area I was working in looking for food!