The parabolic equation (PE) method has been applied to approximate the wave equation, construct radiation conditions, solve scattering problems, construct initial conditions, and derive energy flux conditions. A new application of the PE method, filters based on rational approximations of depth operators, is described and tested. The rational approximation is designed to act as the identity operator on the desired part of the spectrum of the depth separated wave equation and to annihilate other parts of the spectrum. This approach does not require explicit knowledge of the spectrum. The applications of the filter include directly solving eigenvalue problems, annihilating components of the wave-number spectrum, generating initial conditions at the source range, and eliminating Gibbs oscillations that arise in energy-conserving PE solutions.