For nfets where the substrate is not connected to ground, is it required for it to be in its own separate Dnwell (instead of sharing the same Dnwell) for proper LVS in Magic? I tried putting two nfets in the same Dnwell, each in its own separate pwell with each pwell connected to a different net, but after extraction in Magic using the SKY130-supplied Magic deck, the two pwells get shorted together. In order to separate the two nets, I have to put the two nfets in separate Dnwells. Am I missing something? I played around with the isosubstrate tech layer, and it works without Dnwell, and I can separate two substrate connections to two different nfets using it. But when I draw Dnwell over it, the nets get shorted again. What is the proper way to accomplish this i.e. two nfets in the same Dnwell but different pwell nets?

Are you using different pwells in different subcircuits? I had problems with extraction without flattening everything.

@Robin Tsang: Feel free to post the layout to me and I can look at it. In principle, this is supposed to work and shouldn't require flattening; magic determines the pwell, nwell, and substrate areas from the top level being extracted. If that's not happening, then it might have something to do with the hierarchy, but there should be ways to solve it within the hierarchy that don't necessitate flattening.