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To request confidence intervals from a model, simply include a call to mxCi in the model, and add "intervals=T" to the call to mxRun()
themodel <- mxModel(themodel, mxCI(c('model.A'))) mxRun(themodel, intervals=TRUE)
The interval and type defaults give the 95% upper and lower CIs that most users will want.
the reference list is quite intelligent, and can take: matrix or algebra names, matrices with column and row indices. So the following are all fine, as long as they are legal objects found in the model or its submodels.
mxCI(c('model.A', 'top.A[,1]', 'myAlg'))