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Are you using CosmosWorks or FloWorks? You can use mesh refinement with CosmosWorks in the areas of interest but there are limits.
I'm using CosmosWorks Pro. I haven't even bothered trying to refine the mesh where I need because I know it would either fail (due to the high numbers of elements) or take forever. I don't want to have huge run time especially when I'm just at the beginning of the project.
I am currently working on a thermal simulation for an LED where the ration of LED Chip to Heat sink is pretty big. I got around this problem by using a mixed mesh and creating shells for the smallest elements. Shell meshing will created a 2D elements instead of the 3D solid element used in a solid mesh. Using shells is a little more complex as you have to create bond contact gaps between the shells and the solid bodies. So far I have been able to obtain the same results (to a certain degree of accuracy) between a solid mesh vs. a mixed mesh.
Hope it helps