In　order　to　faithfully　investigate　the　microscopic　and　mesoscopic　structures　of　bulk　metallic　glass　(BMG)　materials,　inhomogeneous　contrast　in　nanometer　to　micrometer　scale　in　BMG　specimens　has　been　throughoutly　studied　by　transmission　electron　microscopy　(TEM),　atomic　force　microscopy　(AFM)　and　scanning　electron　microscopy　(SEM).　It　is　found　that　ion-milling　induced　surface　roughening　and　pattern　formation　are　the　source　of　the　inhomogeneous　contrast　in　TEM　images　of　BMG　samples.　Additionally,　high　resolution　TEM　and　X-ray　energy　dispersive　spectroscopy　investigations　rule　out　structure　or　composition　changes　in　the　specimens.　The　dynamic　roughening　process　during　ion-milling　as　well　as　saturated　pattern　sizes　are　revealed　from　Zr-,　Cu-,　Fe-　and　Mg-based　BMGs.　The　understanding　of　this　inhomogeneous　etching　in　BMG　specimens　is　critical　for　recently　intensive　TEM　studies　on　microscopic　and　mesoscopic　inhomogeneities　of　BMGs.　(C)　2012　Elsevier　Ltd.　All　rights　reserved.