Shinto Alter

My family is Catholic, however, my mother is Japanese and practiced the Shinto religion. She has a Shinto alter in her room. She is recently deceased. What do we do with her alter and accessories?

I definitely would keep her altar!(correct spelling). The Catholic religion is broadminded enough nowadays that you can do that, to honour your mom.. It's nobody business but yours.
http://en.wikipedia.org/wiki/File:Kamidana.jpg

I was raised in a family that was Catholic on one side and Protestant on the other and the family went to either church depending on which side of the family we stayed with. Religion was the only thing they never argued about. After all the first Protestants were Catholics that disagreed with the Pope.

We also had the opportunity to go to a synagogue a few times (Jesus was Jewish all his life, wasn't he?)

The Shinto religion has some common beliefs with the oldest religions of Europe, where I was born, like the Celtic religion, for example.
The first Catholics freely borrowed from the Celts and the Romans, and many European churches were originally holy places of older religions. Some of the Catholic holy days have a Celtic or Roman origin..

Some of the oldest statues of the Virgin Mary in Europe were originally a Pagan divinity.

Actually shinto altars (kami-dana) are supposed to be renewed once in a while.

Of course, a lot of Japanese families keep them forever, but properly they are to be exchanged to new ones every decade or so, or even each year depending on the region.

In any case, I think it's good thinking for the OP to study about it now, because she wouldn't want to let her great grandchildren carry on the burden without knowing much about it.

If you need to do something about your altar, discuss it with your local shinto shrine. If there isn't one near you, consult with the one you can get contact with.

I wonder if the OP's mother had obtained anything from any shrine lately. If so, that might be a good place to start asking. If not, I don't think she was that strict about her beliefs anyway. God is in the soul of the believer.

http://kamidana.seesaa.net/category/4850531-1.html

Religions originating from ancient RIGVEDA tend to put consecrated items into flowing water--the sea or a river or a pond sometimes breaking them up before submerging them.