How to remove flakes caused due to application of Minoxidil?

There are a couple of options you can consider. First, if you are not using the minoxidil foam try switching from the lotion drops to the foam.    This helps some individualsI suspect you'll want to try a few different things (or even a combination of things)1. Try shampooing daily2. Use a shampoo with salicyclic acid a few times weekly3. Try other anti inflammatory shampoos including those with selenium sulphide, zinc pyrithione and tar4. Reduce minoxidil to once daily for a period of timeThe flaking in and of itself is not harmful. I appreciate you want to get rid of it, but don't worry that itnis somehow causing harm. 

If you have flaking, the I suggest that you use an anti dandruff shampoo which can be very effective at addressing the flaking. Head and Shoulders is a good starting point