CUBIT usually relies on the ACIS solid modeling kernel for geometry representation; there is also mesh-based geometry.   Other solid model kernels are planned. Geometry is imported or created within CUBIT. Geometry is created bottom-up or through primitives. CUBIT imports ACIS SAT files. CUBIT can also read STEP, IGES, and FASTQ files and convert them to the ACIS kernel. SolidWorks, AutoCAD, and some other commercial CAD systems can write SAT files directly.

Once in CUBIT, an ACIS model is modified through booleans. Without changing the geometric definition of the model, the topology of the model may be changed using virtual geometry. For example, virtual geometry can be used to composite two surfaces together, erasing the curve dividing them.

Sometimes, an ACIS model is poorly defined. This often happens with translated models. The model can be healed inside CUBIT.