In case you missed John W. Martens' post on "The Good Word" on the Scriptural roots of purgatory, check it out here. A sample:
Purgatory has had an odd history, with many Catholics today no longer having a clear sense of what it is. And while many Protestants have long rejected purgatory as a non-biblical Catholic "thing," many of the Reformers of the 16th century, while they may have had troubles, to put it mildly, with indulgences or ecclesiastical organization did not initially struggle with the reality of purgatory. The basic reason, I think, is that it makes theological sense. In order to be in the presence of God one must be prepared; since God’s being is holy, one must be made ready to be in the presence of holiness. This is the process of purgation, or purification, in which the remnants and effects of our imperfections and sins are burned away.