What does Hebrews 9:3 mean?

The writer of Hebrews is giving a brief description of the old covenant's system of sacrifices and worship. The purpose is not only to show that the prior system was limited and flawed, but that its elements were meant to be symbols of God's eternal plan: the ministry of Jesus Christ. That symbolism is the key point of this passage, rather than the minute details of the temple's arrangement (Hebrews 9:5).

As described in the book of Exodus, the tabernacle—the tent—where God commanded Israel to perform their ritual sacrifices included a particular area separated from the rest of the structure. This "Holy Place" contained a seven-flamed oil lamp (Exodus 25:31–40) and a table which always featured twelve loaves of bread (Exodus 25:23–30; Leviticus 24:5–9).

Also within this section was another, curtained-off room called the "Most Holy Place." The difficulty of translating from one language to another can make this reference confusing, especially when reading straight through from verse 2 to verse 4. According to the pattern given in the Old Testament, the altar of incense is in the Holy Place. Read as typically translated, in English, this phrasing seems to suggest the altar of incense is in the Most Holy Place. However, the structure of the Greek here suggests a parenthetical statement. It's entirely possible that verse 3 is meant as an aside, or a footnote, by the writer of Hebrews. This would connect the reference to the "Holy Place" with the golden altar of incense, with the comment made in verse 3 intended as a separate, parallel reference. Alternatively, the Greek term used in verse 4, echousa, is typically a reference to possession, not position. In other words, the writer might have been saying that the altar "belonged" to the Most Holy Place, in the sense that their purposes were connected, not necessarily that one was inside the other. It's also possible, if not likely, that the priests used more than one altar for various purposes in their daily duties.

Regardless which is the case, the writer of Hebrews makes it clear that his description is very brief (Hebrews 9:5), so any confusion over what is meant should be viewed with that approach in mind. The point of this passage is to show the symbolic meaning of these items, not to give their exact placement or position.