Bones are really commonly used to connect with the past. Though, I have heard of people finding bones of their spirit animal and using them in a dream pillow to connect with their spirit animal through dreams. You could also connect with the Deer since bones do have a bit of that being energy still.
You can also build a relationship with the Deer to help you in your magical practices. You can connect with Deer by through meditation, dreams, etc...
I am not too sure on how you would clean the bones. Though I have read (somewhere, forgot) that you never use bleach because it destroysthe structural.
If the bones still have flesh on them, leave them out till the flesh decomposes or put the bones you want to keep into some water and let it slowly rot. Once you can pick the bones clean, you will need to soak them in peroxide till they get white enough. Keep an eye on them, the peroxide can work very fast. If smell will be an issue as the flesh decomposes, you can burry the deer bones and check on them every few months.
Venison is common in my house hold, my family members and myself are seasonal hunters and i learned at a young age how to use as much of the deer carcass as possible. One way that i have used is boiling the bones in salt water its much easier to remove the flesh but its not always the best solution but it certainly does it. The trick is to remove as much of the skin and meat from the bone as possible, use a sharp knife to make short work of it. Bones as mentioned above already can be used to connect yourself with that animal and was already well said i must say. So Honoring the animal by placing it on your altar is something you can do, some members of my family even make tobacco pipes out of bones. Antlers are interesting to they can be clanked together to echo sound throughout the forest to attract certain spirits as well as draw in energy, so keep that in mind, but also be aware it may attract other Buck's. Best of luck! Misanthropy wrote a post in Magic Items similar to this question, shouldn't hurt to take a look! Blessed be.
The above posters have already given really great information/ideas, but I'll just toss some stuff in because I do work with bones. As an animist, I believe it's important to check with the animal and see if it's okay to use their bones, but that depends on your beliefs.
Here's a forum post I wrote on bone reading that tells how to divine with and cleanbones: https://www.spellsofmagic.com/read_post.html?post=920804
You can use bones in spiritwork, as said above. You could also use them to tap into the energy of deer in general.
You can make tools from bones. I have a scapula I use to hold an offering cup and a bone wand. I've also used skulls and vertebrae as candle holders. You can also just use them to decorate your altar. It's a great way to draw in the energy of the animal and to allow yourself to connect with death energy. I like to use them to balance out my altar (some plants for life, some bones for death).
You can use them as talismans corresponding to the energy of the animal. For example, if you found the bones of a doe, you might find themto have a gentle, motherly energy. You could use this to help calm you during times of stress. (Just an example.) You could wear the talisman as jewelry if you wished.
You could also use certain bones in corresponding spells. If you cursed someone, for example, you could use teeth to give the curse some bite.
Some people use bone powder as an ingredient in various things. The purpose ofthis may vary depending on the recipe.
I've also found that sometimes you can sit and hold a bone and just feel out something to do with it. Not always, and it's totally fine if that doesn't happen with these bones, but I've had time where I pick up one of my bones and just feel like I should make a certain things with it or preform a certain spell.
Other than that, I think doing a ceremony for the deer sounds very nice. Whether you opt to use them in practice or not, I've found that doing a little thing to honor the animal that passed is nice, and it helps connect you to the process of gathering, cleaning, and working with the bones if you choose to use them.