Suppose you have 12 ml in your tube. Collect 1 ml as each fraction from top using a 200-1000 micoliter pipette and you will have 12 fractions but remember put a yellow tip on the top of blue tip (double tip). Do it gently!

You can puncture the tube with a needle, so they will come out slowly. Then, use a tube with volume markers on the wall (see attached pictures) to collect them. From the indication of the volume markers you will know how much volume it has come out. Microcentifuge tubes can be used for collecting small amount of volume, while the Falcon tubes can be used to collect larger amount of volume. If you want a specific volume, such as 0.3 mL, you can pre-mark a line (for 0.3 mL) on the tube before you use it to collect. 

You can use the Beckman Fraction Recovery System.

You use a normal syringe pump to push a heavy density solution(Fluorinert FC-40) from Sigma) through the tube and then collect the elute into tubes on a fraction collector by drop mode to get same volume into each tube.

Not a cheap option but works very well.

Thanks a lot for your responses.

Have you figured a way to do it by far, Mohsin? Just curious.