All structural analyses apart from static will involve calculation and manipulation of the mass matrix.
In the static case:
kx = f (f = nodal forces, k = stiffness matrix, x = nodal displacements hence no mass matrix needed).
Eigenvalue (modal or free vibration):
kx + ma = 0 (m = mass matrix, a = nodal acceleration)
Dynamic (transient):
kx + ma + cv = f(t) (c = damping constant (Ns/m), v = nodal velocity, m = mass matrix)
I don't know the preprocessor you're using, but why not write out the deck manually and add the *ELEMENT MATRIX OUTPUT manually into the applicable part of the deck. Check in the manual for the correct position of this keyword in the deck, but I believe it should be located within the *STEP module. The matrices will then appear in your chosen file (or .dat if none) file.