Is there a way in Premiere to process a file like logging and capture? I have a list of timecode in and out points for the source footage, (the best takes etc). 

Is there a way to process a file like logging and capture, processing the in and outs and saving as individual files? 

Rather than my current method of using the source monitor, key in the the in point time, then pushing the mark in button, key in the end point time, push the mark out button, the inserting into a sequence. 

I need to cut a file as individual clips based on the list.
Try this:

Create a bin in your project window, lets call it "selected-clips".

Use your source window to mark your "in and out" points then drag that 'clip' into your "selected-clips" bin.

Once you have all your clips in, right-click on EACH clip and select "Make Subclip".

Now, highlight all the 'Subclips', right-click and select "Export Media". A window should appear - add it to a queue - Media Encoder should open - then batch export your 'Subclips'.

Done.