Confocal fluorescence and Raman microscopy are becoming important characterization methods in polymers, especially for blends and films. However, caution must be used in analyzing the data because of the spherical aberration introduced into the illumination and collection of light caused by a mismatch in the indices of refraction of the sample and the design of the microscope objective. In many cases, the measured shape of the region under examination and the measured intensities are rendered invalid because of this aberration. Simultaneously, the axial resolution is degraded because the central light rays and the extreme rays have different focal points. It is shown that the loss of axial resolution can be minimized and the loss in intensity can be either reduced or accounted for. The error in location within the sample and, hence, the shape can be easily corrected.