I know that this is going to sound odd because they're not known for this... but how goes metallica get that clean tone that they use in Welcome Home and One?
Roland Jazz Chorus.
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Roland Jazz Chorus.

This and only this

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I've found the Mesas work quite well for the Metallica sound (Obviously, since that's what they used)

Basically, what your looking for is a dark tone - which the Roland Jazz Chorus provides.
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Roland Jazz Chorus.
This. It's a very good amp, probably one of the best for clean tones. I have a Roland Cube which emulates the Jazz Chorus and cleans are amazing.
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Thanks everyone! But, are there any pedals that would help?

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Roland Jazz Chorus.

This is true, however i found this video:


in which is stated that the cleans are also produces by the Tri-axis.

not having used any of these yet. I don't know the impact caused on the tone.

so yeah there you have it, Roland JC120H and a heavily customized Mesa Tri-axis.
Main gear:
'06 ESP Truckster
Diezel VH4S with Diezel 412F Cab
a good clean channel and a chorus pedal, the boss ce-2 mij does it perfectly
Member of the Schecter Hellraisers
Esp Ltd KH-603, Schecter c-1+ and Epiphone Les Pauls
Carvin amps, Sperzel Trim-Lok, Emg active pickups only, Tonepros bridges.