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So I think you have found a limitation of polygon's in EAGLE. When you are doing a polygon on copper layers you can draw a solid polygon and then within that another polygon set to 'cutout' and that area will be removed from the main copper polygon. However, when it comes to non copper layers you can only choose 'solid' or 'hatched' for the polygon so you don't have any option to cut away the area you don't want. The only work around I can think is to effectively split your polygon into two halves with the two vias sitting exactly on the joining line and the polygons being drawn so they skirt around the vias.
Can I as why you want to do this? Is it because you don't want solder to get wicked down the via away from your thermal pad? If so that wouldn't be an issue if the drill was small enough so maybe you could use a smaller drill and if needed increase your via count. Alternatively you could specify these vias be filled. I'd be worried about trying to use tiny circles of solder mask on top of vias, I'm not sure how well that would work. I've never tried it so it might be fine but it's not an option I had considered previously.
Thanks Rachael for the quick response!
Yes, I was concerned about the solder wicking. Will try your ideas.
I can't figure out how to get my tstop layer to take same shape as my polygon. I'm trying to create a heat sink area beneath a DPAK device. I was able to get the polygon, top layer to take proper shape by naming it same as grnd pad on device, adding a via, and connecting it to ground, then "ratsnest." But none of that seems to be available for the tstop layer. I don't want the parts of other vias and traces to have their copper exposed. For example in the picture the P1 trace and it's via inside the polygon area would have the copper exposed rather than masked.
Can someone help?