If I understand your question correctly first urea is used as a denturing agent to break H -bonds in both protein and nuclei can acid in hence in Denaturing PAGE in Nucleic acids separation it is essential to prevent re-annealing to reform secondary structure pre run is essential to equilibrate the gel and it is essential to remove urea from the wells prior sample loading to insure proper bands

I do not think pre running removes urea from the wells. Manual rinsing out of the wells before samplie loading is important. I think the main reason for pre running is to raise the temperature of the gel system to ensure that the sample remains uniformly denatured. The pre run may also remove small impurities from the buffer and gel but this is less important ensuring uniform electrophoresis conditions for most of the run

Thank you Prof. David Spencer for your valuable time spent for an elaborate reply. It really helped me understand the basic concept.

Thank you Prof. Paul Rutland and Prof.Abdelrahim Hunaiti for your time to clear my doubts... Thanks a lot....