Use a crowbar or shim to remove any trim where the floor meets the walls or cabinets. If the trim is free of mold and not warped or otherwise damaged, remove it carefully so that you can use it again and save a few bucks.
Pull up the existing carpet, linoleum or vinyl with your crowbar.
Check the subfloor for any signs of excess moisture or soft or black spots. If you don't find any, your floor is ready to have a new finish layer on it once you scrape any adhesive or glue off the subfloor, using a paint scraper or other scraping tool.
Remove the portions of the subfloor that are rotten, using a crowbar or a hand saw. Note the thickness of the subfloor material so you can replace it with plywood of the same thickness.
Use a circular saw to cut new pieces of plywood to fit in the rotten places. Install the new pieces by drilling the plywood into the joists under the subfloor. Lay a level down on the installed plywood to ensure the floor is level.
Install self-stick floor tiles over the subfloor. You can use many types of self-stick tiles, from cheap vinyl to more expensive bamboo or composite materials. To install, lay down the tiles in the center of the room first, like the professionals do. Use a razor blade or box cutter to cut any edge pieces to size. Press the tiles down firmly to get them to stick properly.
Replace the trim pieces you removed in the first step by nailing them back onto the cabinets or walls.
