Basically, but I'll let him (her?) say it with his own words.
http://citizenspook.blogspot.com/According to the Constitution, "civil Officers of the United States" may be Impeached. So, for purposes of this analysis, we shall assume that various United States Officers, from the President and Vice President to Cabinet members and others in the State and Justice Departments, have committed impeachable offenses. We will also assume that the House has impeached these Officers after Patrick Fitzgerald's investigative report is released and that the Senate has voted to convict and thereafter removed them from office and that Grand Jury indictments have been returned following the Senate's conviction. And finally, we will also assume that the "sitting" president has issued sweeping pardons for every Officer indicted in criminal court.
This analysis will be limited to situations where convictions/indictments occur after House Impeachment and Senate conviction. Assuming indictments are returned by Fitzgerald's grand jury(s) prior to Impeachment, the president, despite the intense political fall out which is guaranteed to occur, may pardon those Officers involved, even himself. But Congress would still have a duty to Impeach those Officers. Assuming such Impeachments are followed by Senate convictions, all of the removed Officers will thereafter be subject to indictment, criminal prosecution and punishment.
Thereafter, according to a fair reading of the Constitution, criminal court indictments, convictions and sentences may not be pardoned when they flow from "Cases of Impeachment" where the Senate had voted to convict.
In order to avoid a double jeopardy defense, the Impeachment process should be completed prior to criminal trial prosecution and conviction. However, indictments alone do not trigger double jeopardy defenses.
It's well established that presidential pardons cannot overturn the "Judgment in Cases of Impeachment". Such "judgment" is directly limited, by the Constitution, to removal from office and disqualification from ever serving as an Officer of the United States.
The issue which has never been litigated before is: Whether civil Officers of the United States, removed from office by conviction in "Cases of Impeachment", who are later tried and punished in criminal courts, can thereafter be pardoned by the President? This report concludes that the Constitution bars any such pardon.