Remove Doubles on the micro scale

I am having difficulties with remove doubles where vertices that i dont want to merge are merging. I belive this is controlled via Merge Distance or Double Threshold acording to the user manual for 2.6 but I am working with a very small scale. The problem vertices are 53 micro meters apart or .05 mm and when i try adjusting this Merge Distance parameter it does not help, ive tryed typing .001 mm but it defaults to 10 and similar small number values into the box to no eval.

Is this because I am exceeding a program limit perhaps a variable type size or range, or am I incorrectly changing this value. If its a limit is there another way around the problem?

Scale everything up to a reasonable working size, you can scale down at a later stage
It will only merge selected verts, don’t select vertices you don’t want to merge

Thank you, I did not see your response untill now. Your technique of selecting only what I wanted to merge has worked.