The fault classification of a small sample of high dimension is challenging, especially for a nonlinear and non-Gaussian manufacturing process. In this paper, a similarity-based feature selection and sub-space neighbor vote method is proposed to solve this problem. To capture the dynamics, nonlinearity, and non-Gaussianity in the irregular time series data, high order spectral features, and fractal dimension features are extracted, selected, and stacked in a regular matrix. To address the problem of a small sample, all labeled fault data are used for similarity decisions for a specific fault type. The distances between the new data and all fault types are calculated in their feature subspaces. The new data are classified to the nearest fault type by majority probability voting of the distances. Meanwhile, the selected features, from respective measured variables, indicate the cause of the fault. The proposed method is evaluated on a publicly available benchmark of a real semiconductor etching dataset. It is demonstrated that by using the high order spectral features and fractal dimensionality features, the proposed method can achieve more than 84% fault recognition accuracy. The resulting feature subspace can be used to match any new fault data to the fingerprint feature subspace of each fault type, and hence can pinpoint the root cause of a fault in a manufacturing process.