Flow cytometer systems are provided having intermediate angle scatter detection capability. In some aspects, systems are provided that include an intermediate angle scatter (IAS) light detector positioned to measure intermediate angle scatter emitted from a flow cytometer. The system further includes a mask disposed across a portion of the IAS light detector and positioned between the flow cell and the IAS light detector to cover at least a central portion of the IAS light detector so as to block a diffraction pattern observed at the detector. In some instances, the diffraction pattern is created by a flat beam profile irradiating the sample. Methods are also provided for configuring a flow cytometer to block a diffraction pattern created by (1) a flat laser beam profile irradiating a flow cytometer liquid sample, or (2) a mismatched index of refraction between a sheath fluid and a liquid sample in a flow cytometer.