Femtosecond stimulated Raman microscopy (FSRM) is an upcoming technique in nonlinear microscopy which facilitates rapid chemical mapping. It employs femtosecond white-light pulses as probe pulses and intense picosecond pulses as pump pulses. Stimulated Raman scattering (SRS) occurs at the focus of a scanning microscope. Chemical constituents in the sample are identified via their Raman signatures. In this article, disturbing interference patterns in FSRM are reported. They are caused by a broadening of the pump pulse due to nonlinear interactions in the focal region of the microscope and reduce the signal-to-noise ratio. The properties of these modulations are explored, and the methods to suppress them are presented