It would help to know what type of St John's wort you have - there's many different species and hybrids - but now is not a good time to prune any of the shrubby forms.....unless you don't mind losing any more flowers for this season :-)

There really isn't a step-by-step involved. Prune the entire plant back to a few inches from the ground each year in late winter or early spring. The groundcover form can be pruned back at any time and often is done multiple times a season to keep its aggressiveness in check and to remove rust damaged foliage, which is a huge problem in many areas.

I will send you a picture of it as soon as I get a chance.
Yes, I know it has to be pruned in the spring.

I am sending a picture of my St. John's Wort via the 'Name This Plant" forum. That is the only way I know how to include a picture.

Okay, I found out that I could use Photobucket which I am a member. Here is a better picture of St John's Wort with my question.

{{gwi:248121}}

Yes....cut back to a few inches above the ground in early spring. In my climate, I'd bump that up to midMarch.

I live in New York, would I do it in Mid March also?

Here in Philly we cut most hypericum back to about 12" every April.