Bipolar surface EMG (sEMG) signals of the trapezius muscles bilaterally were recorded continuously with a frequency of 800 Hz during full-shift field-work by a four-channel portable data logger. After recordings of 60 forest machine operators in Finland, Norway and Sweden, we discovered erroneous data. In short of any available procedure to handle these data, a method was developed to automatically discard erroneous data in the raw data reading files (Discarding Erroneous EPOchs (DESEPO) method. The DESEPO method automatically identifies, discards and adjusts the use of signal disturbances in order to achieve the best possible data use. An epoch is a 0.1 s period of raw sEMG signals and makes the basis for the RMS calculations. If erroneous signals constitute more than 30% of the epoch signals, this classifies for discharge of the present epoch. Non-valid epochs have been discarded, as well as all the subsequent epochs. The valid data for further analyses using the automatic detection resulted in an increase of acceptable data from an average of 2.15–6.5 h per day. The combination of long-term full-shift recordings and automatic data reduction procedures made it possible to use large amount of data otherwise discarded for further analyses.