In ModelMuse, "Model Features" are data that are only defined at certain locations. Most of them also vary with time. In most cases, Model Features are used to define the boundary conditions of the model. Model Features are treated similarly to Data Sets except that there are no default formulas for Model Features. Model Features are specified only with objects (points, lines, and polygons).

For PHAST, SUTRA, and MODFLOW, the user can specify different times for different Model Features and the times need not correspond to the boundaries of any previously defined stress period. ModelMuse will determine what the stress periods ought to be based on the times entered by the user. Thus, the specification of the boundary conditions is independent of the time discretization specified by the user. The Time-Variant Specified Head (CHD) package in MODFLOW is different from other packages in that once a cell has been specified as a CHD cell, it can not be converted back to a cell that does not have a CHD boundary in it. (This is determined by how the CHD package is implemented in MODFLOW.)

If an object defines a well in the Well package in MODFLOW and the object has more than one section, each section will be used to define a separate set of wells. If two or more sections of the same object occur in the same cell, a single well will be defined for that cell with the total pumping rate being the sum of the pumping rates for each section considered separately.