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We demonstrate the strong influence of GaN substrate surface morphology on optical properties and performance of light emitting devices grown on freestanding GaN. As-grown freestanding HVPE GaN substrates show excellent AFM RMS and XRD FWHM values over the whole area, but distinctive features were observed on the surface, such as macro-pits, hillocks and facets extending over several millimeters. Electroluminescence measurements reveal a strong correlation of the performance and peak emission wavelength of LEDs with each of these observed surface features. This results in multiple peaks and non-uniform optical output power for LEDs on as-grown freestanding GaN substrates. Removal of these surface features by chemical mechanical polishing results in highly uniform peak wavelength and improved output power over the whole wafer area.