Evaluating nanoscale cellular mechanics for disease biomarkers has been challenging due to the significant heterogeneity between cells and other biological structures, which reflects the variability in gene expression. Atomic force microscopy-based methods can visualize these heterogeneities with high spatiotemporal resolution; however, processing large time-dependent viscoelastic data sets is computationally expensive. Here, we introduce a novel viscoelastic method based on a modified Fourier transform, enabling multitime-scale viscoelastic analysis at drastically improved rates (over 37,386-fold) compared to traditional approaches. We used this method to quantify multitime-scale viscoelastic properties of living melanoma cells with varying degrees of malignancy. More malignant cells are softer and more fluid near the nucleus, while the leading edge is stiffer and more viscous, suggesting that regional mechanical effects are critical for enhanced migration. Cellular population heterogeneity analyses revealed that metastatic cells exhibit fluid-like viscoelastic behavior, while benign cells exhibit more solid-like behavior. This new method provides novel label-free biophysical indicators to aid in diagnostic and therapeutic approaches.