Well first I want to thank "rekharam" for bringing this to my notice,since my car was white the lime stain would not be noticed but it bothered me a bit from past 2 months & it looked like bird droppings & I would have gotten the car detailed for around 3500 Rupees just to get rid of this mark.
What you will need is - Pure Lemon juice squeezed into a Glass (Pic attached)
Keep some clean water & cloth to clear some lemon run offs
In the attached pictures the deposit does not look like much but they were thick & my eye would go towards it everytime i walked up to the car in sunlight.
Step 1 - I made sure I had enough tissues with me & proceeded to add a drop of pure lemon juice to see if there was any reaction or side effects,all went well & i could see reaction & bubbles appearing.
Step 2 - After making sure that small drop had weakened the sediment enough to rub it off,I checked if the paint had a reaction to the juice,thankfully none.
Step 3 - I soaked the paper tissue in pure lemon extract & placed it over the stain as it was a curve & the juice would run off.
Step 4 - I used paper tissues to clean the soaked sediments,I had to repeat soaking two times as it was a thick layer(Pic attached).
Step 5 - Use clean water & cloth to wipe off the lemon extract that would have run off,admire your work & stain free car.
(see last pic)
The Culprit - There was water leaking from the roof & it had dripped on to my car roof for close to a day non stop before i noticed(pic attached),I later tied some plastic over the area where the leak is.