Boundary Layers GMSH

How do you add boundaries to a complicated structure in GMSH. Prior to importing it to Fenics.

For my particular project I need to create over a 100 tubes, and be able to model and calculate the external flow as well as the internal flow of the tubes with a penetrable membrane.
The tubes would be stacked in a configuration similar to a radiator on a car.

Right now I have a single tube modeled and then in Solidworks I put them in the configuration I want then export the model to Gmsh. But can’t figure out how to do boundaries on each one. (would prefer to use cylindrical coordinate system if possible)

There are many examples of Gmsh usage in their own tutorials and benchmark, for instance: https://gitlab.onelab.info/gmsh/gmsh/-/blob/master/benchmarks/occ/inner_boundary_layer.geo