Bubbles and applicator marks in polyurethane are usually the result ofoverwork with the applicator (not solvent popping). The coating is notcompromised, but someone who has considerable experience applying clear coatings should not have a lot of trouble with bubbles

Whether you're using a brush or a pad, polyurethane cannot be applied like paint, where you apply it somewhat randomly and then use your strokes to distribute it evenly and smooth it. Polyurethane is thicker than paint and dries quicker, so bubbles can't migrate up and pop before the surface begins to dry and they get trapped under the film. The bubbles are introduced when you rub back and forth with the pad or brush. The analogy for this is to take a wet sponge and put a drop of detergent on it. If you tap the sponge, you might get a bubble or two. If you rub across it, you'll get more bubbles. If you rub rapidly back and forth across it, you'll get a lather. In the same way, if you "mop" back and forth with a pad or brush in the polyurethane, you'll get bubbles. Keep this in mind when you're applying the polyurethane. Now for the remedy:

First, scuff sand the floor with 220-grit sandpaper, as you would between coats. If you still see a lot of bubbles after a light sanding, you may have to sand a bit more aggressively, just until the surface feels smooth to the touch, but you don't need to remove the first coat. After sanding, vacuum off the sanding dust, then remove the dust residue by wiping down the surface with a soft, lint-free cloth (old cotton t-shirts work well) dampened with 100% mineral spirits. You are now ready for the next coat.

Whether you're coating a door, a tabletop or a floor, you'll have more success at maintaining a wet edge and avoiding bubbles and applicator marks by always pulling your strokes in the direction of the boards and wood grain, and in the same direction -- right to left or left to right, whichever is more comfortable for you or appropriate to the project:

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If you make the first pass left to right and the second pass right to left (basically zig-zagging across the surface), by the time you get to the end of the second pass, more time has elapsed since you laid down the beginning of the first pass and it may have begun to dry and will not level as well and may leave a lap mark.
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The technique for avoiding bubbles is to lay the coating down as smoothly as possible in the first stroke and leave it alone to level. Use the widest applicator you can to work more quickly and have fewer overlaps. For a floor, a lambswool applicator is recommended for oil based finish, and a synthetic pad applicator for water based finish. Many professional floor finishers use a tool called a t-bar. For small areas, use the widest brush possible, natural bristle for oil based coatings and synthetic bristle for water based coatings. Load the applicator enough that you may apply a thin coating of finish without having to press down on the applicator to get more out. Overloading the applicator may leave "trails" of product on both sides of the pass where excess squeezes out and the heavier coating will result in heavy lap marks. (You can tap the pad once on the slanted and ribbed part of the tray to release some product if it's too heavily loaded, but don't rub it over the ribs.) Lightly touch the surface with the loaded applicator and then start to move the applicator across the surface in the direction of the wood grain. You may angle the applicator slightly to direct any excess product toward the uncoated surface, like a snowplow, to pick up and distribute on the next pass.

When the brush/applicator stops applying a continuous flow of finish, re-load the applicator and pick up where you left off. This will prevent over-brushing, and working quickly means less dry time before the next pass. Again, as explained above, always pulling left to right (or right to left -- whichever is more comfortable for you) will leave less time for a pass to dry before the next pass. Reducing temperature in the working area will slow down the drying process, allow trapped air to escape, and make it easier to keep a wet edge. Ideal working condition would be between 65 F and 77 F. with less than 50% relative humidity.

Another coat applied using this method should give a beautiful, smooth finish with no bubbles. Stirring too vigorously could introduce bubbles into the polyurethane that would show up in the application. While the flattening agent necessitates additional mixing, polyurethane should never be shaken, and it should be stirred from the bottom of the can (where the flattener settles) to the top, taking care not to introduce bubbles.