Yeah, make sure you copy the entire folder structure from the highest level and DONT delete ANY files (like I did!)
I spent the entire night last night and the last week trying to get compatibility of .MTS files shot on a Canon HFS11 into FCE 4 (FCE 4.0.1 to be exact).
I shot 3 months worth of footage on the HFS11 and would daily dump the AVCHD folders into date folders (ie 06
0110, 07
0110, etc etc) on an external HDD.
Since I had all the .MTS files off the camera I didnt know if I could use Log and Transfer to bring them into FCE but it is possible. Like other forums many people suggested you had to have the folders exactly like they were on the camera. This is true, unless of course you have deleted some files or if any become corrupt then the structure isnt exactly the same. For me I had deleted any junk files using a fast .MTS viewer (called a windows 7 machine!) without realising it was going to affect the 'import' process in FCE.
SOLUTION
I found that the files in the CLIPINF folder (.CLI files) were matched to the .MTS files in the STREAM folder. So if you delete any .MTS files I guess Log and Transfer reads the INDEX.BDM file or the .CLI files and says hang on, something is different. So I went through my .CLI files and found the names missing from the .MTS files and duplicated a colour bar clip I made and renamed it to the missing files. Viola, and FCE 4 could 'import' them.
Im also going to try swapping files and deleting other files to see if you can get a very basic folder structure for anyone who has just the .MTS files.
Cc.