piche, what you described is how I play dvd and blu-ray files.
I too have a Samsung but it isn't 3D.
Here's what works for me, I don't know if Samsung has changed up the way files play on internal media player since mine is about a year or so old.
Anyway, for dvds, I copy main movie to computer hard drive using dvdfab.
Seems the new dvdfabs versions are different now...my version is from the middle of last year.
Then I run the files through VOB2MPG and the output is a single .mpg file
This will play in the Sammy's media player fine.
For blu-rays, it gets more complicated but generally I run it through dvdfab,
selecting entire disc.
To get just the movie part I then use BDtoAvchd, select correct playlist then set it up so it will not do any re-encoding....that part is important.
If you desire to shrink the size any, it is better to use BD Rebuilder.
Now here is an important step...if you are going to use the blu-ray file...at least
on my tv...it doesn't play m2ts at all...check your manual and see if yours does...
if not...I simply rename the .m2ts to .ts and the tv media player doesn't care and plays it perfectly.
You can select MKV extension file in BDtoAVCHD if you would want to try that.
Unless Samsung has changed something, playing from external usb was a mystery as to how to keep it from dropping the power to the usb hard drives.
After much research, I came upon a simple solution for that simply by using a powered ubs port, connecting the ext. hard drive to powered usb then connecting powered usb to tv.
I think that about sums it up...remember dealing with blu-ray files is more complicated...so likely you will have to learn how to do it.