Board Thread:Naruto Discussions/@comment-26993711-20160205011621/@comment-24808887-20160205143209

@Sayian101, one of the cases of Naruto being at his base alone is when Orochimaru sealed Eight Trigrams Sealing Style with Five Elements Seal - that's when he was 100% using only his chakra he still was able to use Multiple Shadow Clone Technique against Amegakure genins still had his large chakra and regeneration(after fight with Kiba) while having "debuff" of distorted chakra control.

In short Base Naruto(or any other character - Base Uchiha, Base A, Base Hyuga) is Naruto who does not use anything: modes, enhancements that can activated and deactivated. That's why for example Base Sasuke is Rinnegan Sasuke. Although any effect of said mode to Naruto which grants him new ability in base counts as base ability, like gain of SPSM allowing to Base Naruto form and use FRS.

About what you said case with Madara's mokuton can't be counted as Base Naruto because there was "activation" he intentionally received chakra from Kurama.