This is most important setting in PLUS RepliCAM. To denote the reference point taken in photograph this setting is used. For that purpose you go to
Menu Settings -> Reference -> Select First Reference Point
Select Second Reference Point....
Or you may also get this from Reference Toolbar as
In this select First Reference Point then mark this on reference point of photograph loaded. While marking take care that both reference point ie of software and reference point on photograph should coincide. There should not any gap between them. When you are marking use window zoom or select RP of software and keep mouse pointer on RP of photograph and press F5, you will get zoom area of that point. Then mark on it. And select other reference points in same way but go in one direction ie anticlockwise. Refer fig given below;
If you mark reference points incorrect order then you'll see the error message as shown below.
Then you can again reset the reference points.
After doing this, click on a sub menu, present
in Reference menu ->Set Reference Rectangle size or click on icon 
present in
reference toolbar. From which you can enter the distance which you take between
references. In this case you will get a dialog box shown below.
In this dialog box if you are not saves standard size then select custom option and enter size. Else select saved rectangle size.