Putrefactio and mortificatio usually refer to two different aspects of the same
stage in the alchemical process and are both connected to death. They are not
considered an alchemical process but are the inevitable result of various
operations on substances which are deemed necessary for transformation to
occur. Mortificatio is represented as a form of torture or mutilation, as in the
Passion of Christ and the death and mutilation of Osiris and is a feeling we all
have experienced more than once in our lives.  Decapitation, another form of
separation, is also a mortificatio that indicates that the ego must be separated
from the archetypal psyche in order to transcend. We must separate the ego
from the collective unconscious, from the energies that initially gave it form, and
learn to discriminate within non-duality, without projecting or choosing one side
over another.  Edward F. Edinger describes
mortificatio of the king or sun at the
archetypal level as “the death and transformation of a collective dominant or
ruling principle.”  Here is where we must slay our dragons and look for what can
redeem us.  The image of God, soul, self needs to be connected back to the
ego consciousness before we can reach any wholeness.  

The loss of psychic energy, the complete deflation of the ego and the departure
of the soul from the body can all be associated with putrefactio and mortificatio.  
Taking, for example, the Waite Smith deck we could have a spread in which the
Four of Swords or the Five of Cups could well signal a stage of putrefactio or
mortificatio.  Sometimes we need to be still, to rest from strife; or just allow
grieving to cleanse our psyche, to help us move on with our lives.

The last two examples are from the Vision Quest Tarot.  Endurance could well
be a form of mortificatio, just like Torment.
Death card from the Tarot of Prague; image from Manly Hall alchemical collection;
photo of Visconti Sforza family emblem by YRobinson.