We present a comprehensive analysis of different techniques available for the spectroscopic analysis of FGK stars , and provide a recommended methodology which efficiently estimates accurate stellar atmospheric parameters for large samples of stars . Our analysis includes a simultaneous equivalent width analysis of Fe i and Fe ii spectral lines , and for the first time , utilises on-the-fly NLTE corrections of individual Fe i lines . We further investigate several temperature scales , finding that estimates from Balmer line measurements provide the most accurate effective temperatures at all metallicites . We apply our analysis to a large sample of both dwarf and giant stars selected from the RAVE survey . We then show that the difference between parameters determined by our method and that by standard 1D LTE excitation-ionisation balance of Fe reveals substantial systematic biases : up to 400 K in effective temperature , 1.0 dex in surface gravity , and 0.4 dex in metallicity for stars with [ Fe / H ] \sim - 2.5 . This has large implications for the study of the stellar populations in the Milky Way .