The LISA Pathfinder data analysis team has been developing in the last years the infrastructure and methods required to run the mission during flight operations. These are gathered in the LTPDA toolbox, an object oriented MATLAB toolbox that allows all the data analysis functionalities for the mission, while storing the history of all operations performed to the data, thus easing traceability and reproducibility of the analysis. The parameter estimation methods in the toolbox have been applied recently to data sets generated with the OSE (Off-line Simulations Environment), a detailed LISA Pathfinder non-linear simulator that will serve as a reference simulator during mission operations. These simulations, so called operational exercises, are the last verification step before translating these experiments into tele-command sequences for the spacecraft, producing therefore very relevant datasets to test our data analysis methods. In this contribution we report the results obtained with three different parameter estimation methods during one of these operational exercises.