In　this　paper,　an　on-machine　error　calibration　method,　covering　error　modeling　and　measurement,　is　proposed　to　evaluate　and　compensate　the　errors　caused　by　the　mechanical　and　optical　system　equipped　in　the　micromachining　center　using　the　femtosecond　laser.　Through　preliminary　tests　by　dicing　silicon　wafer,　it　has　revealed　that　the　squareness,　laser　beam　misalign　and　focal　position　offset,　are　the　main　causes　to　result　in　the　inaccuracy　of　micromachining.　Consequently,　an　error　modeling　method　is　proposed　to　evaluate　the　error　distribution　in　the　workspace,　and　hereafter　a　comprehensive　error　vector　of　the　laser　beam,　combining　the　squareness　errors　of　Z-axis　with　the　laser　beam　misalign,　is　generated　by　the　variable　substitution　method.　Subsequently,　an　increment　error　model　in　the　instant　local　coordinates　is　established　to　satisfy　the　requirement　of　the　programming　method　commonly　used　in　the　laser　machine　tools.　Furthermore,　a　series　of　holes　and　grooves　are　machined　on　the　femtosecond　laser　micromachining　center　to　validate　the　proposed　approach　and　model.　The　machining　dimensions　including　diameters,　distances　and　angles,　are　measured　on-machine　to　identify　the　squareness　errors,　laser　beam　misalign　and　focal　position　offset　according　to　the　proposed　error　model.　Finally,　the　experimental　results　show　that,　comparing　to　the　uncompensated　tests,　the　machining　accuracy　has　been　significantly　improved　with　the　proposed　method.　©　2016　Elsevier　Inc.