Introduction The objective of this study was to determine compound muscle action potential (CMAP) scan parameters and MScanFit motor unit number estimation (MUNE) in patients with amyotrophic lateral sclerosis (ALS) and to compare the results in the abductor pollicis brevis (APB) to those in the abductor digiti minimi (ADM). Methods CMAP scans were recorded from the APB and ADM in 35 patients with ALS and 21 controls. MScanFit MUNE, neurophysiological index (NI), step%, returner%, and D50 were calculated. Results CMAP scan parameters including the returner%, MScanFit MUNE, and NI can distinguish ALS with high sensitivity and specificity. The electrophysiological parameters, with the exception of D50 (the number of largest consecutive differences of recorded responses generating 50% of maximum CMAP), showed more pronounced changes in the APB than in the ADM, even though most of the patients had normal APB/ADM amplitude ratios. Discussion CMAP scan parameters and MScanFit MUNE can be used in the evaluation of denervation and reinnervation and may herald the "split hand" in ALS.