I have had my juvenile milk snake for about 5 months. She will be a year old soon, and she is almost always hidden in her substrate. She eats very well, sheds perfectly, and is completely healthy, but I rarely get to handle her because she is never out. She musks every time I handle her too, which is only once every couple weeks. I am worried that I am not handling her frequently enough to get her used to handling, but I’m afraid that digging her out of her substrate would be very stressful. What would you reccommend?
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How old is the Milk Snake?
Younger individuals or unsocialized adults are very commonly defensive, flighty, musky, and require more time handling to get over that phase.
I reccomend around 10-15 minutes a day of handling, and choice-based handling does not work as effectively for unsocialized snakes. Avoid handling the day before or after a meal and avoid unnecessary interactions while they are in shed.
If digging around in the substrate seems to be stressful for the snake, reduce the substrate thickness slightly and add more hides so that the snake is easier to find without as much searching.
Handling snakes will stress them out reguardless until they become used to us, keep that in mind.
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It amazes me that milks are considered great beginner snakes, not that you are a beginner, but for the very reason you are having trouble with your snake. The constant musking and peeing is extremely frustrating not to mention stinky and just down right nasty! 
I have used those thin surgical gloves in the past when I’ve handled a musky milk. That helps quite a bit. As far as having to dig her out of her substrate, well that’s a stresser for the both of you. So, if I were you I would remove all of the substrate for now and replace it with paper towels or clean unprinted newspaper. In addition I would add more hides and clutter so she will still feel safe even though she can’t burrow. She burrows to feel safe. After you have her above ground it will be easier to find and retrieve her. This way should not stress her out as much so maybe she’ll quit musking so much. Musking is a natural defense for milks so stress just makes the musky milk flow so to speak.
Start working with her a few times a week except for a couple days after she eats. Since the gloves will keep you clean and once the musking stops the handling session should be pleasant. She has to learn that you are not a threat and that you are not going to eat her and then she should settle down, especially at almost a year old.
This will be a learning process for you as well, knowing that she is just trying to defend herself and learning how to retrieve her without stressing her. It will take patience on your part but you have to get her to the point that she doesn’t think you are a predator. Once she figures it out, and she will, the two of you can enjoy each other, or maybe you can enjoy her and she can “tolerate” you! 
The poor little thing probably wasn’t handled much before you got her so she might take a little longer to “de musk.” She’s just doing something that is normal and natural to her……
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