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Microultrasound (micro-US), also known as ultrasound biomicroscope, is able to delineate small structures with fine spatial resolution. However, micro-US suffers limited depth of penetration due to significantly large attenuation at high frequencies. Modulated excitation imaging has displayed the capability to improve the penetration depth, while maintaining the spatial resolution. But the effectiveness of this technique in micro-US has not been fully demonstrated. In addition, the current modulated excitation imaging systems for micro-US are designed for specific excitation method, therefore, lack of flexibility, and are typically bulky and expensive. This paper presents the development of a novel system to achieve modulated excitation imaging with high programmability and flexibility to satisfy various micro-US studies. It incorporates a high-voltage arbitrary waveform generator for producing desired excitation waveform, and a programmable imaging receiver implemented by the state-of-the-art electronics and field-programmable gate array. Test results show that the proposed modulated excitation imaging system can acquire up to 20 dB signal-to-noise ratio improvement and 83% increase of penetration depth in contrast to traditional short-pulse imaging method. In vivo experiment on the dorsal skin of a human hand demonstrates good performance of the programmable modulated excitation imaging system.