Modeling　analysis　of　a　fractal　rough　surface　at　nanoscale　is　established　by　the　method　of　removing　atoms.　It　is　found　that　utilizing　the　standard　data　file　which　contained　the　information　of　atom　and　lattice　and　removing　atoms　according　to　the　boundary　conditions,　a　rough　surface　model　with　fractal　characteristics　at　nanoscale　can　be　established　by　considering　fractal　theory.　The　rough　surface　determined　by　the　W-M　fractal　function　was　prone　to　unreasonable　structure　with　isolating　atom　columns　when　the　atomic　lattice　constant　was　used　as　scanning　interval.　For　a　better　frictional　simulation　of　rough　surfaces　in　nanoscale　by　the　lammps　software,　Fourier　transform　and　filtering　process　were　adopted　to　remove　these　isolated　atom　columns.　During　this　process,　the　fractal　characteristics　of　the　rough　nanoscale　surfaces　can　be　preserved　by　increasing　the　pass　radius　of　the　filter　and　optimizing　initial　structure　with　the　method　of　minimizing　energy.　Experiments　showed　that　this　method　effectively　established　the　fractal　rough　nanoscale　surface　which　is　consistent　with　the　practical　surface.　©　2018,　Science　Press.　All　right　reserved.