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Any subfloor -- wood, tile, concrete or other -- that has had a floor on it before will have residual elements from the previous floor. Make sure the floor is scraped clean of any residue left over from previous flooring before you begin. Make sure any staples or nails are hammered down, and doublecheck by running a 5" or 6" putty knife over the surface. Remove any baseboard or toe moldings.
Skim coat is a Portland cement-based product that fills in seams and other depressions on most subfloors. Mix a small batch of the skim coat according to directions on the package.
Using a straight-edge trowel, spread a very thin layer of skim coat over the seams. Using too much skim coat will have the reverse effect and cause the surface to become even more uneven.
Once the mixture is nearly dry, scrape the excess from the edges, sweep and vacuum. When it's completely dry, you can start laying the new floor.