Systems, methods and technology for authenticating multi-layered objects using encoded signals such as digital watermarking. In one implementation, a value document includes a substrate and a removable overlayer, with a security feature comprising a digital watermark signal printed to cover portions of both the substrate and overlayer. The digital watermark signal includes spatially arranged signal elements forming a frame of reference. Tampering is detected by evaluating offset values associated with the signal elements, where misalignment within the frame of reference indicates tampering. In some implementations, the value document includes a first digital watermark on the substrate with synchronization and payload components, a token with a second digital watermark, and a removable sticker with a third digital watermark. Additional security features include split-mark configurations, tamper mark configurations, holographic foils with overprinted digital watermarks, and fragile tamper-deterrent features that deform upon tampering attempts, causing detectable signal distortion. Other combinations are also provided.