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1) usually end mills made for aluminum are sharper edge rake/clearance and work better than general purpose mills. its bad when end mill dull and aluminum sticks to cutting edge so bad you getting a hammer and screwdriver to knock buildup off
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2) sometimes end mill corners get abrasive wear and bottom of bore is smaller. if you check bore with pin or plug gage and it starts in but doesnt go to bottom of bore, bore is tapered, same with checking keyways you check top to bottom looking for taper usually
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3) when you double end mill stickout amount tool deflection increases 2x2x2 or 8x more. so if end mill stickout of tool holder amount changes it easily effects tool deflection. most take a finish or semi finish and finish cut after roughing if tight tolerance, many consider <.001" a tight tolerance, where .001 to .005" i would say its a more normal tolerance.
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4) many times a precision bore and keyways are +/-.0003" or less tolerance, thats when measuring taper is a bigger concern and often need a new sharp endmill for less taper. when recutting, tool deflection being less often it cuts more than expected
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5) during tool change, tool runout can easily change if tool holder taper is dirty. obviously runout or wobble can effect dimensions
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6) larger bores if parts gets hot the bore will get smaller when part cools off, and if cold coolant sometimes bore gets bigger when part back at room temperature. this is a common concern (temperature control) when doing tighter tolerances. some machines coolant is cold at beginning of work shift and coolant gets hotter during the work shift. also coolant evaporation can have a chilling effect especially when humidity is low. even if coolant system has a temperature control system to maintain +/-1 degree temp, evaporation chilling can be a problem with tighter tolerances and bigger parts