幢 and 栋 are both measure words for buildings and are largely interchangeable. 幢 is slightly more formal and more common in southern China, while 栋 is more common in the north. 座 is another option, used for large or grand structures.
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There is a second reading, chuáng, an old word for a banner or pennant. It survives mainly in the Buddhist term 经幢 (a stone pillar carved with sutras). In everyday modern Chinese the building measure word zhuàng is the only reading you will need.
Left cloth radical, picturing hanging fabric. Anchors 幢 in the original sense of a banner or pendant flag hung on a tall pole. From the banner-cloth came the measure word for buildings (one 幢 of a structure, like a flag-marked unit) and the noun banner itself. Same cloth family: 帽, 布, 席, 帐.
Right 童 supplies the sound (tóng to zhuàng through a historical t-/zh- alternation in this phonetic series). The child meaning of 童 is incidental here. Same phonetic family: 撞 (bump), 憧 (yearn), 瞳 (pupil of the eye).
