The shape of "The Altar" is supposed to resemble an actual altar. This reinforces Herbert's emphasis on poetic structure. Subsequently, some critics have considered this to be just a gimmick and have spoken condescendingly of this technique. However, given that the shape puts focus on both form and content, the effect makes the poem into an artifact; just like the altar it symbolizes.
Then there are the capitalized words: ALTAR, HEART, SACRIFICE, ALTAR. There is a parallel between altar and the poet's heart. An altar is an object upon which a sacrifice is given. To "reare" is to raise it up. The fact that it is a broken altar parallels the poet's own heart. He offers his heart to God, knowing it may be broken or inadequate. He is being humble and asking God to sanctify this broken altar: his heart.
One possible Biblical allusion is:
"I will give you a new heart and put a new spirit in you; I will remove from you your heart of stone and give you a heart of flesh" (Ezekiel 36:26).
It is likely that Herbert's poem alludes to this affirmation of God's covenant with the Israelites but it could also allude to other things from the Old and New Testaments such as lifting (rock to flesh to spirit) those from original sin (following The Fall) or the spiritual connection with Jesus and his disciples (and those who accept him as the Son of God.) This allusion seems just as likely because of the word "workman" (carpenter) and the fact that the poem's shape also resembles a cross. And the cross was the object on which Jesus sacrificed himself. In any, or all, cases, there is a sequence of altar, sacrifice, covenant, heart-as-altar and spirit/heaven.