The most prominent voice for secular thinking in medieval Europe was undoubtedly Franciscan friar Roger Bacon (1214-1292). Even though Bacon was a monk, the experimental work he did led many people to start thinking and believing in natural phenomenon, whereas previously the trend was consider everything the "work of God". In this way he was the first great modern voice for reason over faith and presaged the Enlightenment.
Continuing in the vein of Bacon were such thinkers as Nicholas of Cusa and Rene Descartes who were also men of faith, but who emphasized natural phenomena and reason in their writings, thus promoting a secular view of the world.
In terms of secularist agitation, advocating the removal of the church from authority over daily life and separation of church and state, this was rare in the middle ages because it would have been considered heresy, a capital offense. A typical example of such a person was Reginald Pecock (circa 1395–1461) who was convicted of heresy and narrowly avoided being burned at the stake.
There are a number of philosophers who avoided heresy charges by simply never mentioning the church and focusing entirely on secular subjects, as though the church did not exist. An example is Niccolo Machiavelli (1469 – 1527), who was never charged with heresy, but nevertheless the church banned all of his books. Another such philosopher was Mirandola, who was arrested and escaped execution for heresy only through the influence of powerful Italian nobles.