Granular conductors form an artificially engineered class of solid state materials wherein the microstructure can be tuned to mimic a wide range of otherwise inaccessible physical systems. At the same time, topological insulators (TIs) have become a cornerstone of modern condensed matter physics as materials hosting metallic states on the surface and insulating in the bulk. However it remains to be understood how granularity affects this new and exotic phase of matter. We perform electrical transport experiments on highly granular topological insulator thin films of Bi$_2$Se$_3$ and reveal remarkable properties. We observe clear signatures of topological surface states despite granularity with distinctly different properties from conventional bulk TI systems including sharp surface state coupling-decoupling transitions, large surface state penetration depths and exotic Berry phase effects. We present a model which explains these results. Our findings illustrate that granularity can be used to engineer designer TIs, at the same time allowing easy access to the Dirac-fermion physics that is inaccessible in single crystal systems.