Is there a room in the top of each temple for the Prophet to go to communicate with Heavenly Father and his Son?
The Holy of Holies, also called the “most holy place” in Biblical tradition, is the most sacred place within the temple. The tabernacle that Moses was instructed to build and use while Israel wandered also had one. (Exodus 26:33-34)
In both cases, the room was a place where, once the edifice was erected and dedicated, only the High Priest could enter, and even at that only once a year, on the Day of Atonement, when a sacraficial intercession was offered for all of Israel. According to Biblical record, this was the original resting place of the Ark of the Covenant and the Mercy Seat, or the lid of the Ark. Once the Tabernacle was completed in Moses’ day, the Holy of Holies was where the voice of the LORD came to Moses when he needed direction or discussion with the Creator.
In today’s temples the Holy of Holies is intended for a similar purpose. Quoting Elder Boyd K. Packer,
“hidden away in the central part of the temple is the Holy of Holies, where the President of the Church may retire when burdened down with heavy decisions to seek an interview with Him whose Church it is. The prophet holds the keys, the spiritual keys and the very literal key to this one door in that sacred edifice”
An interesting fact to make note of here is that most every modern temple does not have a dedicated, or specific room called a Holy of Holies. The Salt Lake City temple has the only one set aside specifically for that purpose. There are photographs available of it. Several other earlier temples, such as the Manti or Logan temples may have had one originally but at some point they were no longer seen as necessary. As such those that were existent at the time were converted to small sealing rooms.
Nevertheless, even though there isn’t a specific room set up as a Holy of Holies (except for the Salt Lake Temple), it is understood that a sealing room in each temple has been designated at the time of construction to be used (if needed) for the purposes of allowing the Prophet to approach the Lord. Often the fittings might be subtly more elaborate than the other sealing rooms even in the newer temples (using crystal rather than cut glass in a drawer handle, for example).