According to Roderick, he feared that the medical men "would disturb her body" so he talked the narrator into helping him place her in a coffin and then put her in a vault until they later took her to the cemetery.
However, some believe that Roderick knew what he was doing when he buried her alive. Her skin was rosy enough that the reader could tell that she still had some life in her yet. The two of them had been cursed since birth, from their incestuous relationship, and this was his way of ridding himself of the curse.
Others yet believe that the narrator is also in on the burying her alive deal, and is just as evil as Roderick. Whichever plot seems correct, it all comes down to the fact that Roderick is sick. He is mentally sick, which affects him physically, and he either doesn't know what to do with her, or he intentionally wants to get rid of her. These actions of his just add to the horror of the story, which, after all is what Poe is all about in his stories.
Quite simply, Roderick decides to temporarily entomb Madeline within the house walls because he is afraid of his sister's body being stolen. The way Roderick describes this to the narrator, however, is quite cryptic. Because of the "unusual character of the malady of the deceased" there were "certain obstrusive and eager inquiries on the part of her medical men, and of the remote and exposed situation of the burial ground of the family." In other words, Roderick had the idea that this medical team who was attending to Madeline was very interested in her corpse for scientific purposes. They were even bold enough to find out that the Usher family burial ground was remote enough (whereas they could exhume the body unnoticed). The narrator also admits that the one member of the medical team encountered by his person had a "sinister countenance." Therefore, the narrator doesn't think this idea of the temporary entombment to be an "unnatural precaution."
Another interpretation explains Roderick's not allowing the medical men to touch Madeline as she, being cataleptic, may not truly be dead. In such a cataleptic attack, Madeline could be stiff as a corpse, leading the doctors to believe her dead and send her body to medical studnts for study even though she is yet alive.
In accord with troutmiller, this ambiguity is part of Poe's "arabesque" technique which embellishes the horror.