The linear state-space model is a well-known code-independent method to estimate the contribution of a trapping set (TS) structure to the error floor of low-density parity-check (LDPC) codes. In this paper, we provide an in-depth analysis of this method by incorporating a more accurate model for the incoming messages to the TS structure that takes into account the randomness and the correlation among such messages. Based on this analysis, we demonstrate that both randomness and correlation result in the over-estimation of the failure probability of the TS. We then propose an alternate code-independent technique for the error floor estimation of iterative LDPC decoders that can accurately estimate the contribution of different TS structures in the error floor. Compared to the linear state-space model, the proposed method is not only more accurate, but also more general, in that, it is applicable to any saturating iterative message-passing decoder, symmetrically quantized or unquantized, over any memoryless binary-input output-symmetric channel. The proposed technique can be viewed as the local application of importance sampling (IS) to the message-passing algorithm over the subgraph induced by the TS in the code’s Tanner graph. In the message-passing process, to account for the effect of the rest of the Tanner graph, density evolution along with a simple correlation model is used to generate the messages coming into the TS from the rest of the Tanner graph. Extensive simulations demonstrate that the proposed technique can accurately estimate the error floor of LDPC codes over both additive white Gaussian noise (AWGN) channel and binary symmetric channel (BSC), for a variety of iterative decoding algorithms and quantization schemes.