It looks fine on the top once I peel the masking, but on the underside I see a bunch of splatter burn marks and the masking is all melted to the plywood. This happened to both thick and thin proofgrade plywood, and the burn marks are scorching through the masking on the underside and causing my wood to burn. I set focus everytime, and I cleaned my glowforge today. Any other ideas?
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What you are experiencing is flashback. The laser is bouncing off of the honeycomb trail and reflecting back onto the plywood. It sounds like you are getting more than usual, but it is hard to tell without seeing a picture. Could you share a photo of the backside of a cut where this has happened.
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Here is a picture of medium proofgrade acrylic. The good side is the top and the burned side is the back. I have the same results with plywood (thick, thin). This is a new issue.
I suggest that you insure that the Proofgrade power/speed settings are auto populating. That is too much flash back. If you are certain your fans and optics are clean and that the settings are correct, email Support photos of the flashback along with the date and time of the print. Perhaps support can take a look at your machine logs and make some adjustments.
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You don’t have “Glowforge air filter attached” enabled when you don’t have an air filter, do you?
I do have a Glowforge air filter 
So that’s some good information. And you have that selection enabled?
Let’s assume you do so I can move onto this… Can you try without the air filter? Run the hose out a window? Just as a test to see if you get the same result? Reason is, I’m wondering if this is some sort of airflow issue.
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Have you checked to see if your filter is pulling enough air? If you have been cutting a lot of MDF or medium plywood (that has MDF in the center) it can fill up and clog an air filter pretty quickly.
How would I check it? I tried searching for youtube videos for how to clean the air filter but I couldn’t find anything that would help me
Unfortunately I cannot at this time as temps are in the double digit negatives due to a cold snap. If it helps, the problem reversed itself the next day even though I didn’t change anything. I was cutting some medium PG draftboard and the laser did not cut through the masking on the back even though I use the pins to keep the boards flat and I manually set focus before printing.
Unfortunately, there is no reasonable way to clean it. You need a new cartridge, which is why most of us try very hard to exhaust outside. I saw where one person had a 4" connection in their chimney to connect a wood stove and ran the Glowforge out that.
It is possible to take the cartridge apart by drilling out the rivets but even doing that is problematic to get the right stuff to replace it. In theory, you are supposed to be able to start the fan at low power at first and increase it as the filter fills up, but you need to have the knowledge and attention that most folks use on their second filter cartridge. Also what you cut makes a big difference in the life of the filter cartridge. Cutting all MDF can fill the filter in a week while engraving slate only would have it last for years with everything else is in between.
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@business1 The above is the important takeaway. Your filter’s cartridge may need to be replaced in days depending on what your lasering.
It’s all about how much material you’re removing with the laser. Almost all of that material is going into your filter.
Slate, glass, materials that we etch rather than engrave, those will barely touch your filter. Acrylics, woods, materials that create a ton of particles when engraved, those will fill your filter very quickly.
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There is a very wide range in that list. You have both charcoal and HEPA filters with a prefilter for the bigger pieces. Acrylics will produce mostly fumes so not hit on the HEPA filter a lot, but being very stinky they will add to the charcoal load. Woods will vary a lot based on smoke and gum. Oak has a lot of both and half as bad as MDF while hard maple is very light on the filter, Though in general harder woods make fewer issues some have a lot of gum.
That makes sense, but the cartridge replacements are sold out 
Unfortunately your choices are limited. You can either replace the cartridge or put the hose out the window. I get that it’s cold out, but if you want to use your laser…
I suppose there’s the 3rd option of venting directly into your living/work space? But…
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You could at least run a test print without venting. I don’t even hook up my exhaust host for small prints, even acrylic (and I don’t have the built-in exhaust fan).
I got some 3" thick x 6 " wide foam and long enough to fill my sliding glass window and put a 4" hole in it and did this…
Some aluminium tape to seal it and voila.
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how do i check if the filter is actually full
Sorry, no clue. Back in 2017 I ordered this for Glowforge use. Then when the filter was first released I read about how often everybody needed new filter cartridges and decided I didn’t want that headache.
Visual inspection. It is documented in the support pages.