Engineered hardwood floors are beautiful, and will last for years. The only problem can be the holes from the nails. These can take away from the flooring, but are easily fixed.
Step 1 - Prepare the Area
Clean the floor as you usually would. Follow by vacuuming, to pull up any debris stuck down in the nail holes. You'll then be ready to fill the holes.
Step 2 - Fill the Holes
Dip the putty knife in the wood filler. Start with a small amount. Swipe it over the nail holes and repeat until they are full. Use a rag to clean up excess around the holes. Allow it to dry.
Step 3 - Sanding the Filler
When the wood filler has completely dried, usually 2 hours, sand each spot that you filled to get it even with the floor. Sand gently in a circular motion until smooth. Follow with a rag to remove the debris.
Step 4 - Staining
Use a clean rag and dip a small portion into the wood stain. Apply it to each of the filled areas and rub it in, to get a uniform color. Allow it to dry, and your nail holes have disappeared.