芯出し means to find the center of a work piece during processing, so a 芯出し測定ポイント is simply a "centering measurement point", or "centering point".

I would translate the sentence like this:
モデルから加工位置や芯出し測定ポイントをダイレクトに取得し、ワークと電極の芯出しから加工までをカバーしたNCプログラムを作成します。

Processing position and centering measurement point(s) are directely acquired from the model, and an NC program is created that covers from centering the work piece and electrode to the actual processing.

...something like this. ...kinda hard to tell how to tweak the sentence without more context.