Learn how to prepare a deck for stain or paint. Before you apply stain, make sure the surface is clean (no dust, dirt, wood fibers or grease), dry and free from mildew.When a surface is not clean, stains and other finishes have trouble sticking and may end up peeling.1  Thoroughly sweep the deck to remove all leaves and other debris.2  Liberally apply cleaner using a roller or pump sprayer (wear protective equipment to avoid contact with skin and eyes).hen a surface is not clean, stains and other finishes have trouble sticking and may end up peeling. 1  Thoroughly sweep the deck to remove all leaves and other debris. 2  Liberally apply cleaner using a roller or pump sprayer (wear protective equipment to avoid contact with skin and eyes).