Methods, fourier domain optical coherence tomography (FDOCT) interferometers and computer program products are provided for removing undesired artifacts in FDOCT systems using continuous phase modulation. A variable phase delay is introduced between a reference arm and a sample arm of an FDOCT interferometer using continuous phase modulation. Two or more spectral interferograms having different phase delay integration times are generated. The spectral interferograms are combined using signal processing to remove the undesired artifacts. Systems and methods for switching between stepped and continuous phase shifting Fourier domain optical coherence tomography (FDOCT) and polarization-sensitive optical coherence tomography (PSOCT) are also provided herein.