A CARS system and method for probing a Raman signature of a sample are described. A short femtosecond pulse from one or more lasers is split into two pulses, a stimulus pulse and a probe pulse, whereby the probe pulse is time-delayed with respect to the stimulus pulse. Both pulses can be phase- and polarization-modulated. The stimulus pulse excites a vibronic level in the sample and the probe pulse probes molecular Raman transitions in the sample. A difference in the signals with and without excitation can be used to determine on which molecule a bond is most likely located. This will allow an accurate and sensitive determination of the presence of specific molecules in the sample. The system and method can be used to analyze biological samples and to discriminate between molecules having overlapping Raman signatures.