The device comes with the SURFE²R N1 Control software pre-installed on the internal computer. This forms both the recording and analysis software. The functions of SurfControl include the managing and coding of workflows which represent protocols for SURFE²R assays. Workflows can contain multiple measurements, e.g. using different substrate concentrations or the comparison of transport before and after inhibition. The workflow includes parameters like duration, speed and volume of solution flow during the experiment, the number and sequence of different buffers, the number of repetitions per measurement, the incubation times between experiments and the volume used for rinsing the sensor after an experiment. During the run of one workflow no interference by the researcher is required.

Beside the design of the experiment itself, SurfControl enables the researcher to view and compare recorded traces. The graphical window allows peak detection and the calculation of the peak integrals including baseline subtraction. An additional results window is used for automated documentation of the traces including file name, values for peaks and integrals and the time of measurement. For further analysis, e.g. the fitting of kinetic parameters or the subtraction of negative control currents, the software is capable of exporting the data to the standard file format ASCII.