Just a simple question

In Fux's counterpoint treatise he constantly refers to the perfect and imperfect consonances. Is he referring to the degrees of the scale or relative intervals? For example, he says when moving from a perfect consonance to an imperfect consonance, does he mean moving from the 5th degree of the scale to the 3rd degree? or does he mean that the harmony being played is of a melody note and its fifth followed by another melody note and its third? I guess the latter wouldn't make much sense since the point of the treatise is to teach which note to be used in harmony. But anyway, what exactly is he referring to as the perfect and imperfect consonance?

The first interpretation is, I believe, the correct one, if I understand you properly.

Fux is not speaking of the interval of motion itself in this instance, but the interval between voices.

The consonances in Fux's world of strict modal counterpoint are the unison, third, fifth, sixth and octave. Of these only the unison, fifth and octave are "perfect" consonances. Since his time, the fourth has come to be regarded as a consonance in some interpretations, whereas in the 16th - 18th Centuries whence Fux's tradition comes, the fourth was considered a dissonance to be resolved, usually to the third below it.

When Fux speaks of motion from a perfect consonance to an imperfect one, he means moving from an open fifth, for example (say middle C and the G above it) to a third (middle C and E above it) or sixth (middle C and A above it).