How to measure human efficiency, machine efficiency and organisational efficiency is discussed at length in Operations Management. For gods sake, do not jump to the conclusion that these concepts are not applicable to IT companies. I say so because IT professionals have penchant of living in myths and one such myth is this.
Coming to replying your query. You need to first measure organisational performance on various parameters. Later you need to come to department's performance and then to employee performance. However, it requires lot of study of systems and process of your company. Every company has unique way of working. Therefore, while designing the measures of performance, lot of customisation is needed.
Reply to your 45-word query is vast and the whole thing cannot be typed here. Therefore, feel free to contact me. We will discuss on telephone. I will tell you how few companies rewarded their employees for their efficiency but organisation continued to suffer losses. This was because they gave primacy to people's performance over organisation's. It should have been other way round.
6th April 2016 From India, Bangalore