How do I remove mod podge bubbles from an irregular surface?
Sources of bubbles

Mod Podge doesn't contain solvents that degas and create bubbles in the finish.  If you are getting bubbles in the finish, it's either because of air bubbles that got mixed into the product, or air trapped during application.

Getting rid of bubbles in the product

As Allison C notes in a comment, the product gets a lot more shaking before it ever gets to you than what it got being knocked off the table.  It's a thick liquid, so it can take a while for bubbles to all work themselves to the surface.  If the container sits for a few days, any bubbles should rise to the top.  

The same would apply if you ever decide to stir the contents.  Stir slowly to not introduce air, then let it sit for a few days.

There's a way to speed up getting rid of any air bubbles.  Slowly pour the contents into another container in as fine a stream as you can.  If you want to store it in the original container, pour it back the same way.  For this to work, you need patience to avoid the temptation to speed things up.  Any air bubbles will end up at the top of the product in the container you pour into, where they can easily escape.

Avoiding bubbles in the coating

Even if there are no air bubbles in the product, you can still get bubbles during application.  There are two main ways.  If what you're coating has a lot of surface texture and detail, you can trap air when you apply the coat.  If you use a scrubbing motion with the brush, that can stir in air.  If you are applying a thick coating, air from those sources can aggregate as bubbles.  The coating dries from the outside in, so the surface can trap them.  Even if the bubble pops, the coating may be viscous enough at that point to not flow into the bubble hole, leaving a pock mark.

Techniques to avoid this:


Apply several, very thin layers, waiting between coats for the previous coat to dry enough to be clear.
Try to brush in smooth strokes rather than scrub the Mod Podge into the detail and nooks and crannies.
Inspect for bubbles after each coat.  If you see a bubble or pock mark, that's a sign that you're applying too thick a coat.  

Wait for the Mod Podge to dry so you can see its final form.  Fill pock marks with a tiny drop of Mod Podge at the end of a pin or toothpick, slightly overfilling so the drop is a little raised (it will flatten when it dries).  You probably don't need to worry about pock marks that seem too small to fill; they will get filled by the next coat the same way tiny detail got filled by the first coat.  Wait for that to dry.  

Inspect to see if any irregularity is visible in the surface.  If so, gently dry polish the area with an abrasive scrubbing pad (the abrasive surface is typically a non-woven mesh of plastic like nylon filaments).  If you need something smaller, try a small piece of nylon fabric wrapped around a cotton swab.   You don't need a perfect surface, just no visible ridges; if any irregularities are barely visible, don't worry about them.  Then give it another thin coating, which will hide any minor imperfections.