if thats so, you have 2 options: 1. cleannest but you will beging from the step 0. you import your stl/obj with your geometry in paraview, then you use the connectivity filter, this should in theory (if it is REALLY like bubbles inside a liquid, so no surface overlaps) give a different ID to each surface, so imagine, you have the volume surface will get ID =0 and for each individual bubble (or multiple if they touch each other) will get another ID, then you use threshold and remove the undersired part. 2. you could use (if i am not wrong, i am not the most experience user with SHM) location**s**InMesh https://www.openfoam.com/documentation/guides/latest/doc/guide-meshing-snappyhexmesh-castellation.html#sec-castellation-locationsInMesh you place a point inside your main domain (outside of the bubble, like in the water) and another inside each of the 'air pokets'. it is easier to do, more dirty, but should work, in contrast as i did not use it i can not confirm but you risk that SHM do not ignore the surface of the bubble, it will mesh the two volumes (water and air) but might try to snap to the bubble, and refine over it also.