The Create Workspace tool is accessed from the HexSim drop-down menu. This tool is used to construct a new workspace and grid. The workspace itself is just a collection of folders. The grid file at the top of the workspace defines the workspace dimensions and hexagon size. Only one grid file, and hence one set of grid parameters can exist per workspace.

There are two principle ways to build HexMaps in HexSim. Users can import ESRI Shapefiles or CSV files, or they can use the Generate HexMap tool to construct either empty or attributed files. Empty HexMaps can be attributed later using the Hexagon Editing tool in the HexMap viewer. Using the Generate HexMap tool to construct an attributed HexMap means supplying a bitmap (.bmp) or ASCII Grid (.asc) image file, and specifying several different parameters.

The HexSim GUI will not save scenarios to the disk until they have passed its extensive error checking to prevent results with errors, some of which might be subtle. This scheme necessitates an alternative to saving scenarios, so that works-in-progress don't have to be completed before the program can be closed. This is exactly what snapshots are for. The Take Snapshot tool is accessed from the Scenario menu.

HexSim's Scenario drop-down menu includes a Recover and a Recover All option. Recover allows users to restore the parameter values associated with specific components of a simulation from the data stored on the hard drive

The HexSim drop-down menu has options for importing scenarios, HexMaps, and Barrier Maps.

Sometimes many changes must be made to a scenario all at once. For example, it might become necessary to substitute one spatial data time series for another throughout a scenario. If many events use this spatial data, then doing so one parameterization window at a time can be tedious and time consuming. The Global Assignment tools each allow users to change one type of data throughout a simulation, using a single dialog window.

The HexSim distribution includes a file called HexSimPreferences.xml. This file can be used to change the model's behavior.