The effectiveness and applicability of a parallel fast direct O(N log N) solver for linear systems with block tridiagonal separable coefficient matrices is considered. This solver is applied in the solution of subsonic full potential flows using the Newton linearization and an algebraic fictitious domain method. The time-harmonic electromagnetic scattering by an obstacle is modeled by the Helmholtz equation with an absorbing boundary condition which is solved using a similar fictitious domain approach. Several numerical experiments are performed with the proposed methods in Cray T3E-750 using MPI-based message passing.