The quintessence is the distilled, pure spirit, without dregs. This was desired by all alchemists (and whisky makers, licit or illicit). In Herbert's time this was high science. The image is that once litres of raw material are refined, less than a thimbleful remains.
If you want to see the Calvinist idea of total depravity expressed by a poet and believer considering a life most others thought exemplary, Herbert should be your master.
LOrd, how I am all ague, when I seek
What I have treasur'd in my memorie!
Since, if my soul make even with the week,
Each seventh note by right is due to thee.
I finde there quarries of pil'd vanities,
But shreds of holinesse, that dare not venture
To shew their face, since crosse to thy decrees
There the circumference earth is, heav'n the centre.
In so much dregs the quintessence is small:
The spirit and good extract of my heart
Comes to about the many hundredth part.
Yet Lord restore thine image, heare my call:
And though my hard heart scarce to thee can grone
Remember that thou once didst write in stone