Molecule Man has recreated an entire galaxy with his power. I highly doubt any control over 'his molecules" from Thanos would be a problem to overcome.
Molecule Man is one of those characters whose past history is mired in wildly fluctuating levels, and retcons, so it's difficult to nail down his current power levels.
However, we're talking about a man who was powerful enough to earn comments on his power level from the Living Tribunal, and pre-retcon, was considered one of the only beings on Earth powerful enough to have a chance at defeating the Beyonder.
Post-era, he even surpassed the Beyonders power level once he unleashed his dark aspects, and though Beyonder was no longer considered at his pre-retcon power levels, he was still a reality warping, universal power level being - And Molecule Man exceeded him.
Thanos would be a footnote by comparison if we're talking power level to power level.
The problem with Owen is that he has some pyschological issues to contend with, confidence being one of them. He was something of a loser in his earlier life and has carried htat baggage with him.
However he is still several orders of magnitude beyond the likes of Thanos.
Originally posted by Nihilist
Not by messing with molecules thats for sure.