In this work, we estimate a model of the vertical dynamics of a quadcopter and explain how this model can be used for mass estimation and diagnosis of system changes. First, a standard thrust model describing the relation between the calculated control signals of the rotors and the thrust that is commonly used in literature is estimated. The estimation results are compared to those using a refined thrust model and it turns out that the refined model gives a significant improvement. The combination of a nonlinear model and closed-loop data poses some challenges and it is shown that an instrumental variables approach can be used to obtain accurate estimates. Furthermore, we show that the refined model opens up for fault detection of the quadcopter. More specifically, this model can be used for mass estimation and also for diagnosis of other parameters that might vary between and during missions.