This paper presents a comparison of several Convolutional Neural Network (CNN) models for extracting target signals in highly noisy measurement conditions. Four CNN architectures were investigated. The first comprises six consecutive convolutional blocks while the second employs a U-Net structure. The third architecture introduces a new model inspired by the principles of wavelet transform. It consists of three CNN blocks with varied kernel sizes branching from the input layer before merging into consecutive concatenation and dense layers. The fourth is a Multilevel Wavelet Convolutional Neural Network (MWCNN), resembling U-net but the upsampling and downsampling are replaced by Discrete Wavelet transform and its inverse respectively. To evaluate these architectures, synthetic data were generated using pulse trains corrupted with various degrees of Gaussian noise to simulate measurement conditions with signal-to-noise ratios (SNR) as low as -20 dB. The methodology encompassed the generation and processing of signals with varied parameters: period (5-25 ms), duty cycle (0.1-0.5), and amplitude (1-150 mV). Subsequently, the machine learning models were trained, validated and tested. Finally, the output is processed to recover the signal amplitude before standardisation. The modified MWCNN model demonstrated superior performance achieving a median of 25.9 dB with a mean Root Mean Square Error (RMSE) that decreases with the amplitude of the signal reaching an average RMSE of 0.000128 mV for 1 mV signals. However, for this architecture, the output SNR drops by a factor of 1.23 when the input SNR decreases by 1 dB. All of the architectures exhibited consistency when testing output SNR for different signal amplitudes, periods and duty cycles. These findings indicate that CNN architectures can be used to denoise signals with SNR as low as -20 dB[...]