I have drawn a simple structure in Inkscape (In Ubuntu 14.04, a simple rectangle) the dimensions of the box are 55mm and 53mm (with a finite line width of .010mm) however when I go to print it the dimensions of the rectangle shrink down to 45mm by 35mm. I saved it as a SVG and hit print. I guess there is some problem during printing stage? Any special settings I need to be aware off?

Hi.

Try saving as a pdf and printing from that outside inkscape.

(The 55/45 mm difference seems close to the 90dpi/72 dpi ration by the way, coincidence or not.)