I have a Vitamin D deficiency. I see a kidney doctor because of kidney issues and he checks my Vitamin D level for some reason.
I can't say I ever had any effectis from the deficiency or when I take something for it I never noticed any changes or side effects.

When my Vitamin D level is low he gives me a prescription where I take Vitamin D, 50,000 units. The script tells me to take 1 tablet per week and the script is for 3 months. Then I seem to be ok on my Vitamin D level then it drops for some reason.

He may not be testing the Vit D directly, and is almost certainly NOT scripting for D3, but for D2. D3 is the better quality product.

Vitamin D2 on RX has been found recently to be very ineffective.
See this thread for details and links:
http://neurotalk.psychcentral.com/thread92116.html

Why would you stop it when your levels came up eventually?
Vit D3 is consumed by the body in many biochemical reactions, so a source of it is necessary on a daily basis. We evolved getting our D from the sun. But today we don't get outside alot like we used to in the past. So supplements are needed for most people.

Stopping it will just lower your level again to a low number.

It is best IMO to take D3 daily. This is OTC and YOU control it.
Get your lowest test result from the doctor and figure your daily dose = 1000 IU D3 for every 10 pts you need to raise. If you are overweight, a slightly higher dose may be needed.
So for example, if you tested at 10, then you would need 4,000IU D3 daily to get to 50.

The D2 in the RX is very very old, and was begun before we knew that plant D2 is not active in mammals and people.
D3 can cost all of pennies a day.