To handle the mismatch problems of spatial-domain motion aligned temporal filtering (MATF) in providing spatial scalability, this paper presents a novel in-scale motion aligned temporal filtering (ISMATF) for highly scalable video coding. For each lifting step of ISMATF, the predict or update is carried out at various resolutions in a scale-by-scale way and the operation at higher resolution is designed to embed the operations at lower resolutions to prevent redundancy in frame representation. The proposed ISMATF has several main features, which as a whole differentiates it from other schemes (e.g. spatial-domain MATF, in-band MATF, straightforward multi-resolution MATF) and makes it effective in video coding with spatial scalabilities. These features include 1) Multi-resolution lifting with perfect reconstruction capability; 2) non-redundancy in frame representation, which favors highly scalable video coding; 3) temporal filtering performed in the image-domain of corresponding resolution, which is different from in-band schemes and preserves high efficiency of motion compensation; 4) no mismatch between the encoder and decoder, no matter which resolution is decoded. The proposed ISMATF scheme solves the mismatch problems of SDMATF at low resolution while maintains a good performance at high resolution. It can outperform redundant multi-resolution MATF schemes by up to 1.0 dB at high resolution.