Machine learning is a powerful tool for extracting valuable information and making various predictions from diverse datasets. Traditional machine learning algorithms rely on well-defined input and output variables; however, there are scenarios where the separation between the input and output variables and the underlying, associated input and output layers of the model are unknown. Feature Selection (FS) and Neural Architecture Search (NAS) have emerged as promising solutions in such scenarios. This paper proposes MICS-EFS, a Model Input-Output Configuration Search with Embedded Feature Selection. The methodology explores internal dependencies in the complete input parameter space for classification tasks involving both 1D sensor time-series and 2D image data. MICS-EFS employs a modified encoder-decoder model and the Sequential Forward Search (SFS) algorithm, combining input-output configuration search with embedded feature selection. Experimental results demonstrate MICS-EFS’s superior performance compared to other FS algorithms. Across all tested datasets, MICS-EFS delivered an average accuracy improvement of 1.5% over baseline models, with the accuracy gains ranging from 0.5% to 5.9%. Moreover, the algorithm reduced feature dimensionality to just 2–5% of the original data, significantly enhancing computational efficiency. These results highlight the potential of MICS-EFS to improve model accuracy and efficiency in various machine learning tasks. Furthermore, the proposed method has been validated in a real-world industrial application focused on machining processes, underscoring its effectiveness and practicality in addressing complex input-output challenges.