Smooth the shallow, small scratches out of the vinyl cladding with a piece of fine grit sandpaper or a light grit pad. Buff the area with light pressure until the scratch is not visible anymore. Do not sand heavily or the cladding will develop patches of rough areas. Wear a mask and goggles to protect your nose and eyes from vinyl dust. Clean the area with a damp towel to remove any vinyl dust particles.
Fill deep scratches, gouges and cracks with vinyl patching compound. Put on a pair of leather gloves before using the compound. Remove any debris from the damaged area. Fill the damaged area with a single layer of compound. Let the compound dry, and add another layer if the scratch is very deep. Do not try to paint over the damaged area since it will not fill the scratch. Smooth the edges of the repaired area with fine grit sandpaper to blend it into the rest of the vinyl.
Order a replacement window from the company if the seal is broken on the vinyl and the wood underneath the cladding is rotting. This situation is not a home repair, but a flaw in the vinyl cladding design. Occasionally the cladding is weakened in one of the corners or seams, letting water seep under the cladding and ruining the wood underneath.