An example method of configuring a programmable integrated circuit (IC) in a computer system includes: selecting a first region of a programmable fabric of the programmable IC for implementation of a shell circuit, the shell circuit configured to interface with a bus of the computer system; selecting a second region of the programmable fabric for implementation of an application circuit, the application circuit configured to interface with the shell circuit; providing a fence region disposed between the first region and the second region, the fence region including a set of un-configured tiles of the programmable fabric; generating configuration data for a circuit design having the first region, the second region, and the fence region; and loading the configuration data to the programmable IC.