This dissertation argues that American autobiographies from the eighteenth through the nineteenth centuries typically promote ideological programs, and that with the rise of secularism these programs are often haunted by the negative affects they must necessarily disavow. Through the lens of affect theory, I interrogate the false binary between religion and secularism in autobiographical texts that, from the vantage point of the present moment, seem particularly crucial. The writers in my study--Gustavus Vassa (or Olaudah Equiano), Benjamin Franklin, Henry David Thoreau, and Mary Baker Eddy--all found themselves straddling an emergent divide between secular and religious models of self-transformation. They actively sought new modes of expression in a secular world, and worked to reconstitute and reconfigure their systems of self and their modes of self-narration to cover terrain that no longer had a clear language or certain categories. This dissertation contributes to recent intellectual debates about the role of religion and secularism in a post-9/11 global economic world, a debate made all the more shrill in the context of wars in Iraq and Afghanistan, the War of Terror, and the Arab Spring. And yet it does so by tracing the debate back to an earlier moment when the process may have been messier, though the debate less polarized. This study mobilizes affect theory in an attempt to get at the public feelings engendered by autobiographical self-portraits consciously attempting to create others in their own molds. It seeks to trace a connection between nation, post-nation, and self-narration in an increasingly secular world. From the mid-eighteenth-century on, American autobiographical texts attempt to organize emotion for the purpose of reasonable, rational self-reform, self-consciously adopting what critics have only recently been theorizing as "secular affect" (Mahmood). Moreover, they do so in a way that explodes the commonsense distinctions between subject and object that a genre like the autobiography would seem to rely upon. Like earlier spiritual autobiographies in which religious affect structures a teleology of conversion, these systems of self, as I call them, are meant to sway converts to the cause, be it capitalist accumulation, secular reason, or the promotion of nationalistic agendas. Systems of self bundle subjectivity, ideology, and affect into attractive lures, creating model subjects to be admired and emulated. To this end, they provide readers with concrete methods offering the promise of self-transformation, giving them practical steps to take so that they, too, can achieve the idealized secular subjectivity advertized by the autobiographical narrator. Just as these texts mobilize affect towards teleological ends, however, they are themselves mobilized by the affect they must necessarily deflect, a move that is all but invisible when one adopts a critical lens assuming that the secular stands binaristically-opposed to the religious. The constitutive disavowals of secular and religious modes of being give systems of self an alternative structure, one that can contradict or compete with the sequential presentation of a life story advertizing teleological ends. Haunting the ideology of progress in these autobiographical texts are the traces of unrecoverable losses, wells of unacknowledged, incalculable affect. This study reads these traces as the sorrows that capitalism, industrialism, and the rise of secular civil society leave in their wake, and as the aspirations for a better world than the narrative of secular progress would seem to provide. American literature is replete with the figure of the optimistic, idealistic, and earnest autobiographical narrator--a subject able to ingeniously and benevolently reflect the infinite possibilities of secular progress. This project argues that such optimistic autobiographical presentations are often constituted in tandem with an intense negativity driven underground--but glimmering out from within the subterranean depths of the text, emanating from within the structures of the systems themselves.