remove outside part of Isosurface bubble
 

I have a zero isosurface with two disjoint parts. Basically one bubble inside another bubble. How can I completely remove the outside bubble/isosurface and leave the inside one intact if they have the same scalar values? Slicing through the isosurfaces gives me a peek inside them, but I would like to completely remove the outer layer.

If one bubble have a value which the other one does not have, you can clip by scalar to remove one of the bubbles.

they all have the same (zero) value.

If there are complex interwoven structures which have to be separated in Paraview, it may be a good idea to produce a special value (just one more array) while producing the simulation data. Let this value be "InnerBubble" in your case and whenever a point of the inner bubble is simulated, its InnerBubble is set to 1. If a point of the outer bubble is simulated, its InnerBubble is set to -1. Then the bubbles can be separated very easy by the clip filter as mentioned above.

Thanks,

I ended up doing it two different ways. It turns out that the outer zero values correspond to small or zero gradients, and the inner layers correspond to large gradients.
Based on the gradients in one approach I simply changed some of the datavalues. Probably your suggestion would be more appropriate, to use an extra variable instead of changing simulation data values.
I also tried using threshold filter based on gradient calculator in paraview. This worked out nicely, except it slows down the visualization.