A robotic system comprising: an input device (108, 109); a non-volatile memory; an articulated instrument; one or more other articulated instruments (231, 241); and a processor configured to: receive information of a first fixed preferred pose for the articulated instrument from the non-volatile memory, the first fixed preferred pose predefined by at least one of an instrument type of the articulated instrument and a current operating mode of the articulated instrument; generate a first preferred pose by using one of the first fixed preferred pose and a dynamically changed version of the first fixed preferred pose, the dynamically changed version of the first fixed preferred pose generated by automatically changing the first fixed preferred pose according to information of the one or more other articulated instruments (231, 241); generate a commanded pose of the articulated instrument in response to operator manipulation of the input device (108, 109); cause the articulated instrument to move towards the commanded pose; generate first force commands for a plurality of degrees of freedom of the input device (108, 109) so as to increase as a difference between the first preferred pose and the commanded pose increases; and command application of the first force commands on the plurality of degrees of freedom of the input device (108, 109) so as to phase in their application according to a first activation signal that increases in magnitude over a transition period. an input device (108, 109); a non-volatile memory; an articulated instrument; one or more other articulated instruments (231, 241); and a processor configured to: receive information of a first fixed preferred pose for the articulated instrument from the non-volatile memory, the first fixed preferred pose predefined by at least one of an instrument type of the articulated instrument and a current operating mode of the articulated instrument; generate a first preferred pose by using one of the first fixed preferred pose and a dynamically changed version of the first fixed preferred pose, the dynamically changed version of the first fixed preferred pose generated by automatically changing the first fixed preferred pose according to information of the one or more other articulated instruments (231, 241); generate a commanded pose of the articulated instrument in response to operator manipulation of the input device (108, 109); cause the articulated instrument to move towards the commanded pose; generate first force commands for a plurality of degrees of freedom of the input device (108, 109) so as to increase as a difference between the first preferred pose and the commanded pose increases; and command application of the first force commands on the plurality of degrees of freedom of the input device (108, 109) so as to phase in their application according to a first activation signal that increases in magnitude over a transition period. receive information of a first fixed preferred pose for the articulated instrument from the non-volatile memory, the first fixed preferred pose predefined by at least one of an instrument type of the articulated instrument and a current operating mode of the articulated instrument; generate a first preferred pose by using one of the first fixed preferred pose and a dynamically changed version of the first fixed preferred pose, the dynamically changed version of the first fixed preferred pose generated by automatically changing the first fixed preferred pose according to information of the one or more other articulated instruments (231, 241); generate a commanded pose of the articulated instrument in response to operator manipulation of the input device (108, 109); cause the articulated instrument to move towards the commanded pose; generate first force commands for a plurality of degrees of freedom of the input device (108, 109) so as to increase as a difference between the first preferred pose and the commanded pose increases; and command application of the first force commands on the plurality of degrees of freedom of the input device (108, 109) so as to phase in their application according to a first activation signal that increases in magnitude over a transition period.