ATMEL Mega1284P evaluation board avalible

When Eagle complains about "Clearance" errors around the regulator thermal pad, do I need to resolve that or can I ignore it as the top & bottom layers are intentionally connected together with vias?

I'm thinking this needs more work - looking closer, the top layer has a small pad in the middle that is isolated with an outer pad that is connectet to the ground hatching.
The bottom pad is VCC, but is also connected to the bottom layer ground hatching.
I need some way to isolate the regulator thermal pad.