Yes you are correct about Thomas.

My question is, What was his rank in the US Army in April 1861?

It seems to me that most of the senior officers, those who you would expect to be the most informed as to the events from a military stand point of 1861, abandoned the United States army and left nothing but middle level managers like Major's and Captain's for the United States army to rebuild on. And half of those regular army Major and Captains in 1861 also when to the South.

As I said, I have found only one officer beside Winfield Scott who held rank higher that the grade of Major. And that was Col. Phillip St George Cooke. And even half of his family members went to the South. Does anybody know of another Colonel or higher rank in the regular army in early 1861, that remained with the Union?

I know that people made decisions for different reasons, mostly personal. And Thomas always comes up as a Virginian that remained with the Union.

But the jest of my inquiry is the abnormally high number, in my estimation, of senior army staff that resigned and joined the Confederacy. This mass migration is always explained away as being the same simplistic explaination that is given for Lee's resignation that they were all southerners and their loyality to their home state became greater than their loyality to the US Army and the United States.

These men were professionals in every sence and were considered by the US ARMY, prior to their resignations, as the best soldiers that the United States Army ever produced, to that date. And many such as A. S. Johnston and Robert E. Lee are still considered as among the best.

In fact it would seem that Lee was the last major Officer, of high rank, to leave, everybody else was already gone. Did the others see something developing that they did not like, or as men could not abide? Did they see the Constitution being desolved before their eyes? Did they see a government attempting to start a war against their fellow Americans without just cause? And could they support that war?

Thomas, as you point out, is the exception to that rule. So if there is one exception to a rule you have to wonder why there were not more?

Do you see what I am saying? Even Gen. Irwin McDowell, who was the Union Army Commander, at 1st Manassas/Bull Run, doing the same job that Lee would have beeen doing, was only a Captain in actual rank, breveted to the rank of Major in the Inspector Generals Office under Gen Samuel Cooper in April 1861.

Was there nobody else better left?