Make accurate measurements using the caliper, a micrometer or any precise measuring tool depending on the desired accuracy. Be careful with the tolerances. Some 3D printers are extruding more material for the outer shells of the print, especially for small inner holes of the printed part. You know your 3D printer best. Think in advance. for example, if you measure with the caliper a 3.5mm hole that would fit an M3 bolt, maybe it would be a good idea to draw a 3.7mm hole on your design. This unless you have an SLS or SLA printer or you are using a CNC mill to drill it in aluminium. 

Draw the new design using the numbers you obtained from the measurements. I used AutoCAD for this example but there are plenty of solid generating softwares out there. 

Export the newly created solid to STL by slicing it using one of the existing applications on the internet. I am metioning just a few examples for those who are new in this thing. You can tru Slic3r, Cura, Repetier, but there are others available too.  

Print the newly created part.