Normally blisters are not that big of an issue to be concerned with. Unless you have alot of them , They are unusually big  or they are broken. If the blisters are broken then prompt attention is needed to fix them because they can be a source for leaks. It should also be noted that blisters bigger than a baseball should be fixed by a roofing contractor who does foam roofing.

Blisters are fixed as a part of a routine roof re-coat.

In this first picture it identifys a golf ball size blister.

Step 1.

Cut the blister out using a razor knife (bread knifes work the best).

This is a golfball sized blister

Step 2.

Fill the hole with a polyurethane caulking. DO NOT use any other kind of caulking your repair will fail.

Use polyurethane caulking to fill the repair area.

Step 3.

Tool the caulking with a piece of cardboard or putty knife. Make sure you tool the caulking past all of the edges.

Tool the caulking

Step 4.

Coat the repaired area with an elastomeric roof coating. This is a permanent repair.

This is the same process a roofing contractor will use to fix blisters that are baseball sized or smaller and less than a 1/2 inch deep.

Below is a picture of a blister that you should not attempt to fix. If you have one that is broke and might be leaking you can caulk it then have it repaired later.

Volleyball size foam roof blister