Big-Data systems are increasingly important for solving the data-driven problems in many science domains including geosciences. However, existing big-data systems cannot support the efficient processing of self-describing data formats such as NetCDF which are commonly used by scientific communities for data distribution and sharing. This limitation presents a serious hurdle to the further adoption of big-data systems by science domains. This paper presents Kaleido, a solution to this problem by enabling big-data systems to efficiently store and process scientific data. Specifically, it enables Hadoop to directly store NetCDF data on HDFS, and process them in MapReduce using convenient APIs. It also enables Hive to support queries on NetCDF data, transparent to the users. Moreover, it employs optimizations tailored to scientific data, particularly dimension-aware layout which allows efficient execution of subset queries targeting any dimension of the multi-dimensional data. The paper presents a comprehensive evaluation of Kaleido using representative queries on a typical geoscientific dataset. The results show that Kaleido achieves substantial speedup and space saving compared to existing solutions for storing and processing NetCDF data on Hadoop, and it also substantially outperforms the state-of-the-art solutions for supporting subset queries on scientific data.