We present the largest currently existing subarcsecond 3-5 $mu$m atlas of 119 local ($z < 0.3$) active galactic nuclei (AGN). This atlas includes AGN of 5 subtypes: 22 are Seyfert 1; 5 are intermediate Seyferts; 46 are Seyfert 2; 26 are LINERs; and 20 are composites/starbursts. Each AGN was observed with VLT ISAAC in the $L$- and/or $M$-bands between 2000 and 2013. We detect at 3$sigma$ confidence 92 sources in the $L$-band and 83 sources in the $M$-band. We separate the flux into unresolved nuclear flux and resolved flux through two-Gaussian fitting. We report the nuclear flux, extended flux, apparent size, and position angle of each source, giving $3sigma$ upper-limits for sources which are undetected. Using WISE W1- and W2-band photometry we derive relations predicting the nuclear $L$ and $M$ fluxes for Sy1 and Sy2 AGN based on their W1-W2 color and WISE fluxes. Lastly, we compare the measured mid-infrared colors to those predicted by dusty torus models SKIRTOR, CLUMPY, CAT3D, and CAT3D-WIND, finding best agreement with the latter. We find that models including polar winds best reproduce the 3-5$mu$m colors, indicating that winds are an important component of dusty torus models. We find that several AGN are bluer than models predict. We discuss several explanations for this and find that it is most plausibly stellar light contamination within the ISAAC $L$-band nuclear fluxes.
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