Methods and systems for generating high energy, mode locked, femtosecond and picosecond laser pulses are disclosed, including generating electromagnetic radiation from a pump laser; coupling the electromagnetic radiation to a rare Earth doped fiber using a pump/signal coupler; coupling the output from the rare Earth doped fiber to a first fiber; coupling a bandpass filter to the first fiber output and to a second fiber; coupling a first in-line polarization controller to the second fiber output and an in-line polarization beam splitter comprising a non-polarization maintaining fiber output and a polarization maintaining fiber output configured to emit an output laser pulse; coupling a polarization insensitive isolator to the non-polarization maintaining fiber output of the in-line polarization beam splitter and to a second in-line polarization controller; coupling a third fiber output to the second in-line polarization controller and to the pump/signal coupler. Other embodiments are described and claimed.