A counter module system is provided, which may allow for partial or full self check-in by a passenger at a transportation facility, such as an airport. The system may comprise a counter module having multiple bays each for receiving an equipment module. An equipment module may be compatible for installation in some or all of the bays. Easy customization of equipment may be achieved by installing the desired equipment in an equipment module and then rolling the module into an open bay in the counter module. The modularity may also allow for easy access to equipment for maintenance or resupply. When a piece of equipment stops working, the module containing the equipment may be removed from the bay and either quickly repaired or replaced with another module. The system may also have features for providing proper alignment of an equipment module within a bay of the counter module.