A finish can form bubbles only when it is drying, and a professional refinisher usually takes care of them before considering the job complete. They are more common with a water-based polyurethane product than a solvent-based one because the water-based product tends to foam and dry more quickly. If the floor wasn't professionally finished or a few bubbles escaped notice, you don't need to remove the finish to get rid of them.
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How Bubbles Form
Water-based polyurethane floor finish is a milky liquid that is much thinner than a comparable solvent-based product. It tends to foam when you shake, stir and pour it, and while the foam eventually disappears, it may leave a few residual bubbles. When you spread the finish across the floor with a paintbrush or paint pad, you often spread the bubbles with it. Water-based finishes dry so quickly that they sometimes harden before the bubbles have a chance to pop and level out. The result can be a pattern of fully- or partially-formed bubbles scattered over your floor.
After the floor finish has hardened enough to sand it, refinishers pass over it with a floor buffer fitted with a 120- or 150-grit sanding screen to remove bubbles before applying another coat. The process is called screening, and it's one you can use on any existing finish, not just a new one. Like sanding a piece of furniture with fine sandpaper, screening knocks down the old finish, smooths it out and scuffs it so that a new coat of finish will adhere better. Screening does not create much dust and requires little preparation other than ensuring the floor is free of wax.
How to Screen
Rent a floor buffer and screening attachment, and purchase one or two 120- or 150-grit sanding screens from the rental shop. Hook the attachment onto the buffing machine, place the sanding screen face down on the floor and lower the machine onto it. Hold the machine steady when you turn it on, or it will spin away from you. Let the machine ride over the surface of the floor, moving back and forth in an arc and along the walls. After you've screened the floor, vacuum the dust off and wipe the floor with a damp cloth.
Spreading a Bubble-Free Finish
Use a simple technique to spread a bubble-free finish. It requires the use of a weighted, tubular floor finish applicator on a long handle, much like a weighted squeegee without the water scraper. Pour the finish carefully in a line along the direction of the floorboards, and drag the applicator through it. Keep it on the floor at all times, even when you turn, and hold it at an angle so material trails off one end. Pour more material as needed. Dragging the finish in a continuous motion across the entire floor greatly reduces the likelihood of bubbles forming.