Ultra-trace identification of the limited quantity of diluted analyte solutions requires the condensation of target analytes utilizing the superhydrophobic analyte enrichment effect and are extremely desirable for improving the detection sensitivity. Herein, the identification of ultra-trace analyte concentrations employing laser-textured palladium-gold (Pd-Au) hierarchical superhydrophobic micro-arrays as surface-enhanced Raman sensors (SMA-SERS) is reported. The double ns-laser fast scanning strategy produces hierarchically arranged micro-strip and micro-pyramidal arrays over the large surface areas composed of nano-scale inter-particle gaps, enabling the numerous three-dimensional plasmonic hot-spots due to the uniform formation of Au nanoparticles' aggregates/clusters. Under the optimized fabrication parameters, the resultant hybrid SMA-SERS sensors exhibit periodic micro-pyramidal arrays with excellent inherent superhydrophobicity (Contact angle, CA∼171°) and consequently superior SERS performance with uniform (RSD∼10%) signal detectability down to the ∼34.2 fM (3.42×10−14 M) MB molecules utilizing analyte enrichment effect. The accumulation of analytes within the smaller dried spots (Contact diameter, CD∼1.13 mm) results in increased spatial density of analytes and subsequently enables the ultra-low detectability of MGO, DTTCI, PA, AN, adenine, and l-tryp molecules down to ∼3.57 pM, 0.34 fM, 0.31 nM, 0.44 µM, 0.25 nM, and 97.7 nM concentrations, respectively. The multiplexed identification of target (AN and adenine) analytes is explored utilizing serial-deposition of analytes and depict the simultaneous detection of target analytes down to ∼10−7 M (AN) and 10−9 M (adenine) concentrations. The double ns-laser fast scanning strategy provides dual-scale surface roughness in the SMA-SERS substrates and offers ultrahigh sensitivity for the identification of the low amount of analytes utilizing the superhydrophobicity-induced analyte enrichment effect.