The present invention relates to compact, low noise, ultra-short pulse sources based on fiber amplifiers, and various applications thereof. At least one implementation includes an optical amplification system having a fiber laser seed source producing seed pulses at a repetition rate corresponding to the fiber laser cavity round trip time. A nonlinear pulse transformer, comprising a fiber length greater than about 10 m, receives a seed pulse at its input and produces a spectrally broadened output pulse at its output, the output pulse having a spectral bandwidth which is more than 1.5 times a spectral bandwidth of a seed pulse. A fiber power amplifier receives and amplifies spectrally broadened output pulses. A pulse compressor is configured to temporally compress spectrally broadened pulses amplified by said power amplifier. Applications include micro-machining, ophthalmology, molecular desorption or ionization, mass-spectroscopy, and/or laser-based, biological tissue processing.